I installed everything with Bottles. SKSE, BodySlide, FNIS all worked. I could have used Mod Organizer 2, but I prefer to install mods manually.
The only problem I had was the way Kubuntu handles folders. Kubuntu (and other Linux distros I assume) allows two folders to have the same name if the first word in one folder is uppercase and the first word in the second folder is lowercase. This broke some mods, but once I realized what the problem was, I moved all the files to the appropriate folders and the rest was smooth sailing.