Same problem here, installed SkyrimSE + Anniversary Upgrade, installed SkyUI 5.2 via Vortex, but it doesn´t loaded ...
Game and mod-folder are on the same harddisk, installed mod be marked green, but game is still vanilla ...

SkyUI wasn't working for me either. I found a solution that did make it work for me.

Go to "Users/yourname/AppData/Local/Skyrim Special Edition" and copy the files within the folder.

Paste the files in "Users/yourname/AppData/Local/Skyrim Special Edition GOG".

So I just copied and pasted from the folder to the other folder and then SkyUI worked. I guess the files needed get saved to the wrong folder for the GOG version? I don't know, but it worked for me.

OMG, this man should be hired as support, he managed to make my game run with mods for the first time! Unbelievable!

I have searched for hours for some solution. You made me happy.

GOG, next time make things a bit obvious how to handle the new version!

SkyUI needs SKSE (GOG-Version) from skse.silverlock.org. Do you have it in your game folder?
You need to remember to start the game through SKSE-exe (skse64_loader.exe).

In order to make Vortex setup HARDLINKS and put the Mod Staging Folder on the correct drive.
Do these steps...

In Vortex
First, Go to SETTINGS----->INTERFACE

Turn On
Deploy Mods when Enabled
Enable Mods when installed (in current profile)

When that is done, do the following steps, slowly and carefully, DO NOT Skip a step.

1. Go to the Left Column---->MODS
2. Click PURGE MODS, wait until it's finished.
3. Go to SETTINGS---->MODS
4. Click SUGGEST then wait until it's finished.
5. Click APPLY
6. Change the dropdown from SYMLINK to HARDLINK, Click APPLY, wait until it's finished.
7. Go to Left Column---->Mods
8. Click DEPLOY MODS
9. Start the game.

Thank you, it already works, but maybe it will be useful to someone else.

Hi I am new to GoG. I purchased Skryim SE and cannot load the mods. What exactly is Vortex? Do I need to install mods through Galaxy?

"Go to "Users/yourname/AppData/Local/Skyrim Special Edition" and copy the files within the folder.

Paste the files in "Users/yourname/AppData/Local/Skyrim Special Edition GOG".

So I just copied and pasted from the folder to the other folder and then SkyUI worked. I guess the files needed get saved to the wrong folder for the GOG version? I don't know, but it worked for me."

That was the solution: The GoG-version seems to be handled by Vortex as a new game.
Thx for the help to all!

Vortex is a tool that helps in the process of installing mods. It was develop by people from nexusmods.com.
You can use other tool but Vortex supports GOG-build of Skyrim right from the beginning. I think Mod Organiser 2 was also updated to support Skyrim from GOG. So you can use MO2 instead.
You don't need Galaxy to run Skyrim and it is not possible to instal mods via Galaxy.
You will probably also need SKSE from https://skse.silverlock.org/ (pick version for GOG game 1.6.659).
Unfortunately at the moment some mods doesn't support GOG version of the game. Especially the mods who inject their own plugins for SKSE.

I don't have that folder, I made a fresh install. I only have the folder Special Edition GOG. can you upload yours?

Run the game to generate them

Does anyone know a workaround to get FNIS working for the GOG version of Skyrim? I've tried a few times using MO2, always get "2 warnings" and if I ignore the warning, CTD! It seems that FNIS is obsessed with "Steam" and even if you point it to your GOG version, it just warns you then crashes. I checked on the Nexus and the author of FNIS retired in March 2020! I looked at Nemesis, but I just want FNIS for the bouncy KS hairdos and Nemesis does not seem to have any hair mods

has MO2 installed it properly, I installed fnis manually as Wrye Bash wouldn't install all the files & it does work. I just get 1 warning about not being in a steam folder which can be ignored.

FNIS author added some sort of DRM check years ago to prevent users with an illegal copy of the game (at that time only available on Steam) from not being able to use it.
Now that Skyrim is available on GOG, maybe it will also be flagged as illegal.
However, FNIS/NEMESIS is not required.

Physics mods require "Faster HDT-SMP", which was recently updated to 1.6.640 (Steam), it doesn't work on 1.6.659 (GOG). Author is already aware of the situation, but it was unclear whether they intend to make a GOG version or not.