Game won't open with folders

I can't add folders into my mods folder and it's making it super difficult to play. Anytime I add a folder the game simply won't open, but if I put the mods in said folder directly into the mods folder it'll open? I'm trying to organize my mods so I can do the 50/50 method easier but this is making it impossible. I also don't have an error file (or at least I can't find it) since the game just won't open.