After Struggling hard and some trial and error I finally managed to get it to work.
It seems that it depends on your system's language. Which require a little editing for ini's location path.
For me it looks like this C:\Users\Admin\OneDrive\Dokumenty\My Games\Skyrim Special Edition GOG\Skyrim.ini"
Admin is replaced with my pc's admin as instructed of course. But this finally fixed SSEEdit :)
So if it doesn't work for you like it was in my case, then replace Documents with your system's launguage.
For Polish version it's Dokumenty. But if your system is in english then it should work with no editing i guess.
Hope this helps someone who is also having hard time in getting it to work.

Still getting "fail".

The folder \Documents\My Games\Skyrim Special Edition GOG\ contains THREE ini-files. A Skyrim, SkyrimCustom and a SkyrimPrefs. All of these three have the affix(es) .ini.based and a second file with .ini.baked.

I tried the one for Skyrim, but that removed control of the mouse. I'm not eager to re-try.

TYVM

Another alternative is to open Command Prompt with Administrator rights
Type:
mklink /d "C:\Users\[Your Username]\Documents\My Games\Skyrim Special Edition" "C:\Users\[Your Username]\Documents\My Games\Skyrim Special Edition GOG"
Press enter
this will create a symbolic link, which acts as a fake directory pointing to the actual one, this should solve the issue for any other programs as well