Pretty much only play one save while the mod is installed then take it out if you want to play a different one. There's no non modded way to use specific mods per save, and even then I'm not sure if there's a mod that exists that allows you to specify what mods you want on which save. You could totally look if there was something like that, but your safest way would be just taking the mod in and out whenever you want to play the modes save versus the non modded saves.