I have a really simple perk mod with no new scripts or anything that can't be created within the CK itself, so obviously it doesn't use SKSE. It's an .esp file, not a .bsa. It works fine in vanilla but doesn't seem to do anything in SE, and I have no idea what the problem could be.
EDIT: Nevermind, I figured it out. The game was ignoring Nexus Mod Manager and the fact that I had the file in the data directory. I had to go into the game's load order menu and manually check the box saying I wanted to use the mod.