Ah yes.
Mod Manager is used to turn mods on and off. You have to link it the location of the mods you use. But you don't have the mods in the right place right now.
They will go in the "contents" folder for atmosphere. Then in contents you make a folder for the game with its title ID and then a "romfs" folder inside that. And then your mods.
Your mods you download will most probably have the correct structure all ready to drag and drop into contents.
So example,
contents/01007EF00011E000/romfs/Actor/Pack/GameRomCamera.sbactorpack
Also, when you copy some mods over you need to restart your switch before they'll work.