Update: Confirmed to be Working for Dual Wield AND 1 handed + Shield, BUT ALSO NEED TO put ANOTHER set of HKS_SkillAnimA.hkx 10KB version AND HKS_SkillAnimA.hkx 11KB version in their corresponding folders! READ updated info below!

I CANNOT stress this enough, READ THROUGH THE WHOLE THING YES WHOLE THING before doing the TEST! 

While not mandatory, I really suggest having a MMO mouse with 12 thumb buttons, or the Azeron gaming Cyro or Cyborg, makes life so much easier but up to you.

You NEED use the mod https://www.nexusmods.com/skyrimspecialedition/mods/92667?tab=posts the Jedi Apprentice mod and activate it for the esp and other stuff obviously.
This way you can use TWO DIFFERENT movesets per STANCE within the Stances mod!!! Here's how READ CAREFULLY!

This is a very general example so you know what one is getting into, very detailed (at least I think so) explaination after this below.

1. Two separate movesets are in the Neutral Stance folders 9451000 and 9451050( you would have to create 9451050 yourself), along with their other special moves between 9451000 and 9451005 (if you have movesets that have like special move attacks etc).
2. To switch in game, first you have to be in NEUTRAL stance while holding greatsword (cause 9451000 is for greatsword). 
3. To switch movesets WITHIN THE SAME STANCE, for me the hot key skill button is currently set to ; key. To change it go to mod config in menu and find hot key skill section
4. Sometimes the hot key skill may not load and you may have to go to the hot key skill section and under maintenance click load settings
5. May have to change keys the mod can be slightly buggy. I found a workaround that works so far well for me *knock on wood* read below.
but yay! This is usuable with the STances Mod that lets you switch between 2 stances within 4 stances as long the current esp load order is something like this, which works for me:

There may be other esps between them, but as long it's similar to this, should be fine. 
Dodge MCO.esp
Hot Key SKill.esp
Cancel Attack.esp
Attack_dxp.esp 
Stances-Dynamic Weapon Movesets SE.esp
For Honor Power Attack.esp

DETAILED EXPLAINATION BELOW! REALLY MUST READ! To make it clear, I try to separate stances and movesets as two different things, even though they both contain different movesets/animations.

For the Hot Key skill mod, you MUST use the settings loader here https://www.nexusmods.com/skyrimspecialedition/mods/92843 along with the MAIN mod 
and follow the instructions below to do a TEST on ONE weapontype to make sure it works before you go full blast.
- THis is so you don't do all this work below for every weapontype, then find out it doesn't work and come here to get mad at me xD. ALWAYS TEST FIRST!

The Apprentice mod lets you use two separate movesets per "stance" within the stances mod if you follow the below detailed instructions for other weapontype animations!
so basically it acts like this:
Stances mod
- Stances Neutral Stance > Apprentice mod moveset 1 or 2 switch using hot key skill key (for me it's ;)
- Stances Low stance > Apprentice mod moveset 1 or 2 switch using hot key skill key (for me it's ;)
- Stances Mid Stance > Apprentice mod moveset 1 or 2 switch using hot key skill key (for me it's ;)
- Stances High Stance > Apprentice mod moveset 1 or 2 switch using hot key skill key (for me it's ;)

So for every 1 STances dynamic movesets stance, you get two movesets to choose from. 2 x 4 = 8

That's the FIRST STEP how you get 8 movesets per weapontype. The next step is to make sure to add HasMagicEffect("SWApprentice.esp" | 0X000800) OR NOT HasMagicEffect("SWApprentice.esp" | 0X000800)  to the two moveset mod folders PER STance of the STANCES (one is hasmagic, the other is NOT hasmagic) in their _conditions.txt and put the TWO versions of HKS_SkillAnimA.hkx  in the correct folder.

- TO BE MORE CLEAR, let's use Greatsword folders as an example cause there are LOTS of greatsword animations. 
If using the Full Folder Structure mod (which one should be already), under greatsword, you would have the following default folders:

9051000, 9052000, 9053000, 9054000 these are the default folders. I personally added four more with the numbers 9051050, 9052050, 9053050 and 9054050. 
These four new ones will be the new folders for the switch movesets within stances

9051000 and 9051050 are the NEUTRAL stances folder, they do NOT need the HaPerks condition. 

Then put NOT HasMagicEffect("SWApprentice.esp" | 0X000800) [you most likely will need "AND" before that unless it's the first line] in the _conditions.txt of ONE of them, 

I strongly suggest the 000 one. Then put HasMagicEffect("SWApprentice.esp" | 0X000800) in the _conditions.txt of the other one. I suggest the 050 for consistency because it matters for last step!
So the _conditions.txt in 9051000 looks like this:

IsActorBase("Skyrim.esm" | 0x00000007) AND
IsEquippedRightType(5) AND
NOT HasMagicEffect("SWApprentice.esp" | 0X000800) 

and the _conditions.txt in 9051050 looks like this:

IsActorBase("Skyrim.esm" | 0x00000007) AND
IsEquippedRightType(5) AND
HasMagicEffect("SWApprentice.esp" | 0X000800)


9052000 and 9052050 are the LOW stances folder. BOTH the _conditions.txt in this will need HasPerk("Stances - Dynamic Weapon Movesets SE.esp"|0x0004251A) and any other conditions you need.
Then put NOT HasMagicEffect("SWApprentice.esp" | 0X000800) [you most likely will need "AND" before that unless it's the first line] in the _conditions.txt of ONE of them, 
I strongly suggest the 000 one. Then put HasMagicEffect("SWApprentice.esp" | 0X000800) in the _conditions.txt of the other one. I suggest the 050 for consistency because it matters for last step!

9053000 and 9053050 are the MID stances folder.  BOTH the _conditions.txt in this will need HasPerk("Stances - Dynamic Weapon Movesets SE.esp"|0x00042519) and any other conditions you need.
Then put NOT HasMagicEffect("SWApprentice.esp" | 0X000800) [you most likely will need "AND" before that unless it's the first line] in the _conditions.txt of ONE of them, 
I strongly suggest the 000 one. Then put HasMagicEffect("SWApprentice.esp" | 0X000800) in the _conditions.txt of the other one. I suggest the 050 for consistency because it matters for last step!

9054000 and 9054050 are the HIGH stances folder.  BOTH the _conditions.txt in this will need HasPerk("Stances - Dynamic Weapon Movesets SE.esp"|0x00042518) and any other conditions you need.
Then put NOT HasMagicEffect("SWApprentice.esp" | 0X000800) [you most likely will need "AND" before that unless it's the first line] in the _conditions.txt of ONE of them, 
I strongly suggest the 000 one. Then put HasMagicEffect("SWApprentice.esp" | 0X000800) in the _conditions.txt of the other one. I suggest the 050 for consistency because it matters for last step!
 
THIS NEXT FEW STEPS ARE THE MOST IMPORTANT! After you did all that, you need to put AT LEAST one of HKS_SkillAnimA.hkx 10KB version in one moveset folder 
    that has the NOT HasMagicEffect("SWApprentice.esp" | 0X000800)
and AT LEAST one of HKS_SkillAnimA.hkx 11 KB version in ANOTHER moveset folder that has the HasMagicEffect("SWApprentice.esp" | 0X000800) conditions. I suggest putting them in the same stances though.
These two files are found in the jedi apprentice mod, in folder 80111 for the 10KB version, and 80120 for the 
11KB version.

SO for example, one in 9051000 gets HKS_SkillAnimA.hkx 10KB version, THEN 9051050 (where I put the moveset to switch stance to) gets the HKS_SkillAnimA.hkx 11KB version 
 (YES same name but different size, you won't be able to put them in the same folder anyways, they'll just overwrite each other.) 
No need to do so for the rest of the folders in the same weapontype folders OF THE SAME WEAPONTYPE. So each weapontype will need at least two of those hkx files
- So you don't need to put it in 9052000, 9053000, 9054000, 9052050, 9053050 and 9054050. Just 9051000 and 9051050 in this case.
ALSO VERY IMPORTANT. HKS_SkillAnimA.hkx 10KB version needs to go with the _conditions.txt folder that says NOT HasMagicEffect("SWApprentice.esp" | 0X000800) in this case 9051000
while HKS_SkillAnimA.hkx 11KB version needs to go with the _conditions.txt folder that says HasMagicEffect("SWApprentice.esp" | 0X000800) in this case 9051050
If you GET THIS WRONG, you will switch stance, but it WILL NOT SWITCH MOVESETS IN GAME!!!!
If this confusing for you, think this. Apprentice smaller version NOT big enough(heh). Starkiller Bigger version(hehe).

When done and if working properly, when you use neutral or another stance (low, mid, high), you use ; or w.e. hotkey you set to in the mod configuration it will switch movesets WITHIN the same stance. 

I suggest to avoid problems, go to hot key skill menu in mod config
- Go to maintenance, and do this first. Press Reset settings, even if you've never use the mod. Close the menu, open and go back in again. Then make sure Enabled id checked.
- Loading delay set to 0 or 1. Then Load settings on Reload is checked. Then in key Config, set the First skill key to w.e you want (I chose ; ) Then go back into maintenance and click Load Settings.
- Leave the menu, back into game, then OPEN mod config go back into maintenance and click load settings AGAIN.
- I know it's really annoying, but I did have the issue of the key not working sometimes. After doing this though, all good. Make sure load order is something like above what I said earlier.

If working, lets say you equip greatsword. make sure you are using 9051000 animations. Then when you click the hot key skill button (; for me), your character will do a little swing and then when you attack again, it should be using animations from the 9051050 folder. Open Animation Log to check. Of course, to switch STANCES you use the up, down, left, right arrow keys.

The same for 9052000, 9053000, 9054000, 9052050, 9053050 and 9054050 if all works properly. One uses up, down, left, right arrow keys to switch between 9051000, 9052000, 9053000, 9054000 and ; (my key for the hot key skill mod) to switch between 9052000 and 9052050, or  9053000 and 9053050, or 9054000 and 9054050.

This is the "easiest" way in the sense that in game, you don't need to wear something, which is the second way I'm about to say below.
Yes, THEORETICALLY you can combine both the 1st way AND 2nd way to get even MORE movesets (like 16 per weapontype) per weapontype, but I think that's overkill, but up to you. 

If someone is really that interested in doing so, I'll write up a tutorial to do so sometime next week POSSIBLY.

Update: Confirmed to be Working for Dual Wield AND 1 handed + Shield, BUT ALSO NEED TO put ANOTHER set of HKS_SkillAnimA.hkx 10KB version AND HKS_SkillAnimA.hkx 11KB version in their corresponding folders!

If you cannot understand the reading, example folders in the new updated download section.
 We will take the ONE handed weapon sword for example, it has three possible combinations: Sword only, Dual Sword, and Sword + Shield
 
 The folders are like this by default when using the Full Folder Structure Mod, I've provdided an example folder with the necessary files as an example:
 9011000, 9011100, 9011200, these are the NEUTRAL stance folders for 1 sword only, dual sword, and sword + shield in order.
 
 I then added the 50 folders that represent the movesets you want to switch to within each stance, so now it looks like this:
 
 9011000 with 9011050, 9011100 with 9011150, and 9011200 with 9011250 
 
 in  9011000, 9011100, and 9011200 you need to add the following: NOT HasMagicEffect("SWApprentice.esp" | 0X000800) to their conditions, along with one HKS_SkillAnimA.hkx 10KB version for EACH FOLDER!
 
 in 9011050, 9011150, and 9011250 you need to add the following: HasMagicEffect("SWApprentice.esp" | 0X000800) in the _conditions.txt, along with one HKS_SkillAnimA.hkx 11KB version for EACH FOLDER!
 
If you want to add it to the Low, Mid, and High Stance, you will also need to add either NOT HasMagicEffect("SWApprentice.esp" | 0X000800) or HasMagicEffect("SWApprentice.esp" | 0X000800) to the correct folder but no need to add HKS_SkillAnimA.hkx either versions to those folders.
so basically, 9012000 and so forth until 9014200 do NOT need to add HKS_SkillAnimA.hkx either versions to those folders.
 
The SECOND way is THIS and is simpler, but you will not be able to access the other set of movesets unless you unequip the dual swordsman lock, so it's up to you. you will need this mod instead https://www.nexusmods.com/skyrimspecialedition/mods/102318 Nioh2. The mod author has you wear Dual Swordsman's locks item to be able to use this moveset. 

The difference is instead of adding NOT HasMagicEffect("SWApprentice.esp" | 0X000800) and/or HasMagicEffect("SWApprentice.esp" | 0X000800), 
you add IsWorn("Nioh2DB.esp" | 0x080B) AND for the 050 folders and that's it, along with the has perks so for example.
For example: 
- 9052000 and 9052050 both has the HasPerk("Stances - Dynamic Weapon Movesets SE.esp"|0x0004251A), but the 050 will have the IsWorn("Nioh2DB.esp" | 0x080B) AND in its _conditions.txt

so 9052000 will look like this in conditions.txt

IsEquippedRightType(5) AND
NOT IsWorn("Nioh2DB.esp" | 0x080B)
HasPerk("Stances - Dynamic Weapon Movesets SE.esp"|0x0004251A)

while 9052050 will ook like this:
IsEquippedRightType(5) AND
IsWorn("Nioh2DB.esp" | 0x080B)
HasPerk("Stances - Dynamic Weapon Movesets SE.esp"|0x0004251A)

I do not hate the second method, just prefer the 1st one because while it takes longer to set up, imagine in battle or near battle, you have to open up item menu or favorites menu to equip it, instead of just clicking the hot key. BOTH methods will have a ONE second switch stance time before you can do anything in game, so be careful. Second method has extra time of needing to go into favorites menu or item menu, so some people find that annoying.

Yes, for the 2nd method you can instead of using dual swordsman's lock, you can use vanilla game item, so it's up to you.  This way it's more specific imo.
If something is not CLEAR to you, feel free to ask me.