This guide is for people who have just discovered you can mod skyrim and covers the very Basics on how to mod and create a stable game. When you first discover the Nexus, or any other mod forum, it can be like a kid in a very large mall of candystores. There is so much to take in and you want to try every piece of candy from every single store in the mall. The problem is, that has repercussions. At best your game will be buggy and frustrating. At worst, the game will crash to desktop before you even see a loading screen. Almost everytime I open up the posts in a mod forum I see very basic problems that people are having with any given mod. Sometimes, rarely, it is a problem with that particular mod, usually however, it is a problem with how people are modding THEIR game. A lot of the time the fix is very simple. Fixing and finding solutions to fix your game can be more challenging, depending on the problems. If you follow this guide, it will show you how to fix the simple and less complicated problems.
The first thing you need to know is that mods can and do create conflicts. Every time you add a mod to your game you increase the likely-hood of conflicts. Not all conflicts are bad and some are necassary. However, If they are not dealt with in some fashion they will eventually make your game unstable. How many mods does that take? The answer to that depends on the mods in question. Probably as little as two mods, (in extreme cases). In most cases if you only have 5-20 mods, your game will probably function just fine. Once you start getting beyond this limit, you need to start using tools to create a load order of your mods.
Mods generally have .esp or .esm files that make up a load order. An example of this is Skyrim.esm from the main Skyrim game. If you have the Skyrim Legendary Edition, your load order without any other mods would be: Skyrim.esm, Update.esm, Dawngaurd.esm, Hearthfires.esm, and Dragonborn.esm. This is refered to as the Vanilla Game. The Vanilla game will work together as a somewhat stable game. I say somewhat, because the vanilla game is full of "bugs" and or inconsistencies. There are many bugfix mods that you can add to your game that will fix and improve the playability of your game without adding any serious conflicts. They often do however add to your load order, and at some point you will have to sort the esm and esp files into a load order that works best for your game. This is where modding utilities come into play.
LOOT, or the Load Order Optimization Tool is without question, the first and formost tool you will need. It will look at all your esm and esp files and figure out the optimum order they should load in. This alone will solve many problems people have with mods. The more mods and esm/esp files you have the more important this tool becomes.

Download link here: https://loot.github.io/

More information on Loot and a tutorial by GamerPoets is Here: https://www.youtube.com/watch?v=I35nNK8PWlw

You do need to know what you are downloading and you really do need to read the descriptions of the mods you use, because sometimes they give you information that you can use in conjuction with LOOT to reorder your mods. LOOT all by itself is great, but it isn't perfect. Sometimes you may need to tweak your load order further, and that information is usually in the mod descriptions.
Something I touched on above now comes into play. The main skyrim DLC files, ie: Update.esm, Dawngaurd.esm, Hearthfires.esm, and Dragonborn.esm, are all dirty and have a lot of "bugs" that need to be cleaned. You should clean all new mods you have downloaded, and that is especially true of Skyrim's main update and DLC .esm files. To do this you will need SSEedit. You will also need to watch this video by GamerPoets, It will show you how and is better than any tutorial I could give. This Video assumes that you use Mod Organizer to organize your mods, and even though I will not be talking about mod organizers, it is the mod organizer I recommend and a tutorial by Michael of GamerPoets can be found below the cleaning link. If you use another method of organizing your mods, I would suggest you also watch a cleaning tutorial for that method as well as the method described by gamerpoets, as he will show you some other important, and timesaving tips which I highly recommend.

Download link here: https://www.nexusmods.com/skyrim/mods/25859
GamerPoets Youtube link for cleaning: https://www.youtube.com/watch?v=i50wxDuEnn0

If you wish to try Mod Organizer (recommended) you can get it in the Link below. Mod Organizer 2 and the Original Mod Organizer Legacy are both available in the Skyrim Special Edition section of the Nexus. I recommend getting the latest version of Mod Organizer 2. The Legacy version is here as well, but it will not support Skyrim Special Edition or any other 64 bit games.
Mod Organizer 2: https://www.nexusmods.com/skyrimspecialedition/mods/6194
GamerPoets youtube link for Mod Organizer: https://www.google.com/search?client=firefox-b-d&q=mod+organizer+2+gamerpoets

Now that you have cleaned all your esm/esp files, especially the Bethesda masterfiles, and ordered your esm/esp files with loot you have sucessfully fixed the easiest problems to fix. LOOT must be run everytime you add a new mod to your load order.

The Next Stage of Fixing problems with skyrim is conflict resolution. The easiest and I would say best way for a novice to do this is to download and use Matortheeternal's Mator Smash, found here:
https://www.nexusmods.com/skyrim/mods/90987
With a tutorial found here:
https://www.youtube.com/watch?v=l39VMssZmjE
Run Mator Smash on your load order. It will create the smashed patch. Make sure it is in the correct place and order, LOOT will place it at the end of your load order where it is supposed to be. (Like with everything, there are exceptions to this. But it should always be at or within 2-3 places from the end.) Loot should be run prior to making a smashed patch. If you add a mod to your load order or any time your load order changes, you need to rebuild the smashed patch. This is especially true if you delete a mod from your load order, and be aware that this has negative effects on your game and should never be done with an existing save.

*DELETING MODS*
There is only one safe way to delete a mod from your game. Deleting mods from your game will negatively impact your saved game and the negative effects only get worse as you progress through the game. Except for the method I will decribe below, the only safe way to delete a mod from your load order is to start a new game.

If you download a mod or mods that you wish to try out, keep a copy of your saved game prior to installing the mods. Try out the mods and if you find you can't live with them in your load order then the only safe way to delete them is to delete them and go back to that saved game you made prior to installing the mods in question. You should delete any saves made after you installed the mods in question.
This is the one and only safe way of uninstalling mods mid playthrough.
When you make a save with skyrim your loaded mods are baked into the save. So if you delete a mod from your load order without following the methods above, your save will still try firing active scripts that suddenly have nowhere to go. I am not sure of all the repercussions to this but the one and only time I tried this I ended up with a game that became less and less playable.

*AUTOSAVING*
I highly recommend turning off all the autosave features from the vanilla game. They are buggy and will increase your load times as you progress through the game. Load doors that took a few seconds to load at the start of the game will start taking minutes to load later in the game.
If you find that you can't live without an auto save feature, you can get one here:
https://www.afkmods.com/index.php?/files/file/2099-safeautosave/

This guide is by no means comprehensive. The tools listed within this guide are certainly not the only tools available, but they are among the best tools available. This guide is really aimed at people brand new to modding, but is certainly applicable to whoever wants to use it. The functions I have described are not the advanced functions many of these tools provide and I would certainly encourage new modders to spend some time and get to know the tools better.
One of the beautiful things about using a smashed patch is you can always rebuild your patch, so if you want to experiment with SSEedit, that is the esp to use, though the real truth is that if you screw up any of your mods by fiddling with them in SSEedit, you can simply reload and overwrite them.

*Caution*
alway, always, always write down the name of any esp's or esm's you fiddle with in SSEedit. That way you know which files you changed and CAN reload them without having to figure out which file is responsible for your game crashing.

I will only recommend a few must have mods because they are so very vital to the mechanics of so many other mods. The list is short:

- Usleep, or the Unofficial Skyrim Legendary Edition patch found here: https://www.nexusmods.com/skyrim/mods/71214
(Note: if you don't have the legendary edition there are unofficial patches for the main game and any dlc you do have. If you have all the dlc content for skyrim then you can use the Usleep patch. Special Edition users use Ussep patch)
- Skyrim Script Extender. Because where would we be without it? https://skse.silverlock.org/
(download the latest one. Special edition users need the latest skse64 version)
- SkyUI. Because where would we be without it?
For Skyrim: https://www.nexusmods.com/skyrim/mods/3863
For Skyrim Special Edition: https://www.nexusmods.com/skyrimspecialedition/mods/12604

I am in no way associated with any of the above mods, tools or tutorials, so don't hesitate to give a shout out to all those guys/gals who make our gaming experience so much richer. Without them and all the Mod Authors out there, this game would be a shadow of what it is now.




Download Links in order of appearance:
https://loot.github.io/ Get LOOT
https://www.youtube.com/watch?v=I35nNK8PWlw Loot tutorial
Download link here: https://www.nexusmods.com/skyrim/mods/25859 Get Tes5Edit
GamerPoets Youtube link for cleaning: https://www.youtube.com/watch?v=i50wxDuEnn0 Cleaning Tutorial
https://www.nexusmods.com/skyrimspecialedition/mods/6194 Mod Organizer 2
GamerPoets youtube link for Mod Organizer: https://www.google.com/search?client=firefox-b-d&q=mod+organizer+2+gamerpoets Mod organizer Tutorial
https://www.nexusmods.com/skyrim/mods/90987 Smashed Patch
https://www.afkmods.com/index.php?/files/file/2099-safeautosave/