Like I mentioned, clicking Play in steam opens MO2, not Skyrim SE. When MO2 opens I click Run in the top right with SKSE selected.
In the dropdown, if I choose Skyrim SE Launcher instead of SKSE, it runs MO2 again, like it is in a loop.
It runs Steam OS which is Linux based.
Mods are compatible, I have them working for Skyrim. I have launched the game and see them in the menu etc, the issue is my FPS is low and I want to change the settings but I can't open the Skyrim Launcher because running Skyrim opens MO2 and I have to run it that way using SKSE. Selecting Skyrim SE Launcher from MO2 says I can't have multiple instances of MO2, so it is like it is stuck in a loop from Skyrim SE Launcher, which seems to be set to run MO2 now.