As this is a mod for correcting heel wearer poses, it often gets confused by many to be the mod that 'makes heels work'.    Same as it has long been the case for 'Racemenu High Heels Height Fixes' (RacemenuHH) - for which this mod is a REPLACEMENT.    
In any case, it seems that whenever people have problems with their heels, they come looking for solutions either here, or on RacemenuHH site.   Hence, this troubleshooting guide.    Before messing with anything else, check these steps below:

I.  Sort out your High Heel System.
Over the time, Skyrim has seen a number of High heel handling systems.   And they are largely NOT compatible with each other.   Means you really should be using only ONE of those.    A fair few mods that include heels may list both 'RacemenuHH' and 'Lazy Tools' in the requirements without stating that it is either-or, NEVER BOTH.

I would say the most prevalent system today, is Racemenu . Specifically, its feature called "wearable transforms"  which uses NiOverride library.   High heel shoe mesh files contain a special meta-tag.   Racemenu detects it and lifts the wearer up by the amount specified in the tag.   I would say 99% of SSE mods that include heels, found on Nexus and other sites, use this system.    And as Racemenu is also pretty much the #1 character customization mod, it is practically a constant in most people mod lists.    This mod (Heels Fix) is built to be used with this system and none other.    

Alternatives (which you really should NOT be using)
HDTSSE Physics High Heels Framework - never updated past 1.5.97, and pretty much obsolete anyway.    If you somehow find a mod with heels that need it as master, you can either use HDT High Heels Fix which simply provides a dummy master, or you can use instructions on RacemenuHH page to remove the dependency.    In any case, if you still got HDTSSE heels installed, consider getting rid of it.

Lazy Tools - specifically its 'Lazy Heels' component.    If you are sticking with Enhanced Character Edit SE and thus do not use Racemenu, well, I am afraid you came to the wrong place for your heels problems.   Heels Fix will NOT work with Lazy Heels.   

II. OK, I AM using Racemenu!!!
You need to make very very sure that you have correct versions of SKSE and RaceMenu installed.
When you launch Skyrim, and open SYSTEM menu,  your game  and SKSE version are displayed in lower left corner of the menu.
The SKSE page is pretty self-explanatory.
If you are sticking with SE  (1.5.97), you want SKSE build 2.0.20, and  Racemenu Special Edition v0-4-16.
If you chose to not update past AE 1.6.353 (latest version for which DAR is available), you want  SKSE64_2_01_05 (look in the archived builds section) and Racemenu Anniversary Edition v0_4_19_9
If you have latest Steam AE version (1.6.640), you want SKSE 64  build 2.2.3 and Racemenu AE v0-4-19-14
If you have GOG AE version (1.6.659), you want SKSE GOG AE build 2.2.3 and Racemenu AE v0-4-19-14 GOG.

While at it, make sure you also have the correct version of Address Library for SKSE Plugins.   AE version should cover all 1.6.* game versions.
And proper version of PapyrusUtil SE - 3.9 for 1.5.97 SE, 4.4 for AE up to 1.6.640, 4.4 GOG for the 1.6.659 GOG.

Then, you need to make sure  your skee64.dll is working.   Skee64.dll is part of Racemenu and is responsible for a great many things.
Go to:  Documents\My Games\Skyrim Special Edition\SKSE, 
First, look for a file:   skee64.log  (be sure you have file extensions turned on for 'known' file types in your View settings)
If the file exists and is timestamped same time you last ran Skyrim, then it is probably working. 
But just in case, open it up and check it starts with:   NetImmerse Override Enabled 

If the file does not exist or appears older than last time you ran Skyrim:   look for skse64.log in same directory.
You are looking for lines:
  checking plugin skee64.dll
  ...
  plugin skee64.dll (00000001 skee 00000001) loaded correctly (handle X)   <<< X is a non-0 positive number.
If instead, you see something like:
  checking plugin skee64.dll
  plugin skee64.dll (00000000  00000000) no version data 0 (handle 0)
That means you have a wrong version of the plugin.   Check your installed Racemenu version again.
If you see no mention of skee64.dll in your skse64.log, you are missing the plugin file in your SSE\Data\SKSE\Plugins.   Again, check your Racemenu install.  Could be some sort f mod manager glitch. 

III.  I made sure I have the proper SKSE64 and RaceMenu for my game version!
Before you mess with any kind of correction mod, it is a good idea that you have basic high heels functionality.    Make sure you got some properly tagged heels.    Pretty easy to achieve, as you would have to look real hard to find heels which are NOT properly tagged. 
A mod I can recommend is Newmiller Chain Bikini Heels Gloves Stockings CBBE.   If you do not know how to use AddItem or QUI or console to get stuff, the heels from this mod can be crafted at any forge with no perks, from just 2 leather and 2 leather strips.  (Filter for NHH in crafting menu)

Also, it often makes sense to do your troubleshooting on a brand new game.
Start Skyrim.   At main menu, open console (~), and use command:   coc qasmoke   You will load into a test area as a generic male Nord wearing Iron armor.
You can use showracemenu console command to open character editor.    Switch to a female.   
Suppose you have Misc High Heels Stilettos mod installed.    You can use console command:  help mischeel to get the formIDs of those heels
You will see something like: 
ARMO:  (FE036801)  'MiscHeelsEins - Ebony Rose'  (for you, the ID number in parenthesis will differ a bit)    
Now,  use:  player.additem FE036801 1  command to get the item.   Again, you would need to use the ID in your game)
Or you can do these to get some leather and strips and craft the heels I mention earlier - there is an anvil in the test area. 
player.additem 800E4 2
player.additem DB5D2 2 

If you still got RacemenuHH installed, go into its MCM and disable it.    If you got Heels Fix installed, go into its MCM and disable everything.    Do this while outside.    Then, go into some interior space.    For good measure, save the game, exit game, start it up and load the last save..   Try putting heels on yourself if female, or on a nearby female NPC follower.    It is quite simple.  If you got proper SKSE64 and proper RaceMenu,  putting on heels should 'lift you up' so that heel tip are on the floor, and not sunk into it.

One think to check - though  it would be real weird if that were the issue :
Under your Skyrim SE directory, go to Data\SKSE\Plugins.   Check that you have skee64.dll and skee64.ini, and that skee64.ini has this setting:
bEnableEquippableTransforms=1 

There are a few glitches in RaceMenu that I have personally seen.    They typically happen in first few minutes after loading the game, and usually disappear after 5 min or so, but sometimes can persist.
Losing heels offset when equipping/unequipping some other  armor.   You are wearing heels.   You go into inventory and equip something or take something off - i.e. gloves.    Suddenly, your heels sink into the floor.    Sometimes, you will pop right back up upon closing the inventory.  Sometimes, you stay down.    You have to go back into inventory, and unequip/reequip your heels to restore your heel height.   THIS IS A RACEMENU THING.    It seems to be performance related.    Usually after a few minutes, things 'stabilize' and heel offset is no longer affected by gear changes.

Losing heels offset when entering water.    Go into deep water barefoot.     Use mouse to look up and use forward key to get as high in the water as possible.   Note your swimming height.    That is your 'natural' height.    Try equipping heels in water (or going into water wearing heels).    Sometimes, you will lose your heel offset and sit in water at 'natural' height.    Sometimes you regain your heel offset when emerging from water, sometimes not (and have to re-equip heels).   Again, this often happens mostly after loading.   After sometime, your offset 'stabilizes'  and when swimming in heels, you are definitely floating 'higher'.   

Losing heels due to other mods interference.   This is a real gray area, as some mod combos can result in weirdest things.   For example, if you have Mu Joint Fix installed and also Yamato Scabbard Remastered, if you equip the version with SMP tassel, your heels sink.    Somehow Mu Joint thinks it is your hands touching the ground, not the tassel, decides that you are lying down, and kicks in its heel cancel feature.    This is just one example of mods clashing like that, and with people running 500+ mod lists,  tracking those cases down can be near impossible.

IV. Ok, my heels generally do NOT sink anymore!
So, you got proper SKSE/Racemenu, and when you put heels on, you get lifted, and looking great when you walk around.    But, when you sit down, your butt hovers several inches above the chair!      Now, we FINALLY get to the point where you need the heel correcting mod.    Which is what Heels Fix is.   
IMPORTANT:  If you are still using 'RaceMenu High Heels Height Fixes' (RacemenuHH), you need to get rid of it.    It is a more basic correcting mod, and HeelsFix replaces it.   Don't sweat it though: as of version 1.5.1, HeelsFix includes RacemenuHH detection/elimination feature.

V. I have enabled Heels Fix, and weird stuff is happening.    
First, double check you are not experiencing Racemenu glitches I describe in part III.  Generally, unequipping/reequipping your heels should clear things up.   However, if you suspect that something might be interfering, it is a good idea to enable logging, and see what the log says.
Enabling Papyrus Logging:
Under you 'Documents' Windows folder, go into My Games\Skyrim Special Edition.   
Edit file  Skyrim.ini. You need  to add following section:
[Papyrus]
fPostLoadUpdateTimeMS=500.0
bEnableLogging=1
bEnableTrace=1
bLoadDebugInformation=1
If you have a SkyrimCustom.ini file in that directory,  add the same lines to it as well.

Once you have that, when you run Skyrim, the logs will be under Documents\My Games\Skyrim Special Edition\Logs\Script
The most recent file is Papyrus.0.log.    I personally run a dual monitor setup, and use SnakeTail app to monitor the log in real time.

As of version 1.5.1, HeelsFix also includes a 'Heel Refresh' Illusion type spell.  You can buy it off Lucan in Riverwood or use AddItem  or console to get it.   Cast it on an NPC to cycle their shoes off/on and refresh the correcting effect.  Useful if they sink due to a glitch or after changing MCM settings.

You also should go into Heels Fix MCM and enable the 'Debug Logging' option.    This will make Heels Fix output full report about what it is doing.   Of particular usefulness, upon relevant events, it will mention which overrides are present on the root node of each affected character.    I.e. if you are still seeing overrides from 'RacemenuHH', that's quite telling...   If you have trouble reading the log yourself, you can upload it someplace where I can take a look.    

Hopefully, this article have helped you sort out your high heel issues!!!