Discussion Multiple Micro SD Cards on 3ds

I know this has nothing to do with RPG Maker or making Pokemon games (that's what this area is for though right), but I am looking into hombrewing my New 3ds xl, but I don't want to mess up my regular stuff. I thought I could just have 2 separate SD cards, one for Hombrew one for regular, but what I wanted to know was can I actually use 2 different SD cards (use whichever one when it is convenient) without messing up my 3ds more then homebrew would. Thanks

Also on the topic of RPG Maker, has anybody tried out FES it looks cool but I am skeptical about buying it.