this is really doable on a personal level!
I have split my collection up via US & Euro releases and Japanese releases, (I’ve even gone as far as separating Hacked/Modded Roms & Tanslations) that’s much similar to your separate system idea/needs
you just need to edit your es_systems.cfg accordingly and then create rom folders for the systems you’ve added to the es_systems.cfg
then it comes to theming, I can create some custom ones if your using my theme? (it’s posted in the themes part of the forum)
and questions ask away and I’ll help where I can