I just installed GOG Galaxy for the first time ,and I love it <3 Keeps everything in one place. However, Ive run into a bit of a conundrum.

I have Skyrim Special Edition and Fallout 4, and their script extenders which have their own Executables for launching their respective games. Ive tried to add them into GoG as custom executables for the games, but the settings arent being saved.

Anyone know what Im doing wrong?

Describe in steps what actions you do to achieve that.

When Its figured out, I will. Right now, I cant figure out how to do it at all.

You mentioned trying to do smth and expected settings to be saved.
I qualify it as made actions and asked for its description to see, what's missing or wrong.

For now, you need to do it in configuring window via "Manage installation" => "Configure".
- At the bottom there is a "Launch parameters" subsection.
- Create new launch profile in any way and tick "Default executable" to be used as default when pressing play button, otherwise you need to select it every time(?) via "Additional executables" entry.

Thats exactly what I do, but the new settings wont get saved, making it impossible to launch the games via Script Extenders.

At first glance, it looks like a writing permission problem, like when settings file is located in a system-protected folder.
Have you installed Galaxy to either C:\Windows or C:\ProgramFiles or anything similar? Maybe you're using a restricted account? Does your OS have any notable changes from its default installation environment? Do other games' custom executables can be saved?

If to all of them is negative, some googling only led me worth mentioning to this reddit thread.
Maybe it's just a Galaxy bug that got triggered by something else in your environment.