Buttonmasher

Sorry so late to respond. I've been off the grid for the last week or so. I believe the easiest way is for different systems that use the same cores, simply copy and rename the core and point Launchbox or Retroarch to use that core for that system. I personally don't use Retroarch for MAME because for my tastes, I find it to be overly complex, but some systems such as Gameboy and Gameboy color, just copy and rename the core so one of those systems uses one core, and the other system will use your renamed copied core. Does that make sense? After pulling much hair out and before I figured this out, I actually created whole new directories and copies of Retroarch for each system I had problems with which will work but is probably overkill.

I finally got it working last night but with lots of work. It turns out the only way to use system specific bezels in Retroarch via Launchbox is making each system playlists into it's own Platform. So I had to make each system it's new platform, use a separate copy of the same core for each system, and then point the overlay cfg files within each system config files. The bad part if it all was I have to redownload each systems metadata after already doing so once. After doing this I changed all systems to be listed under the Arcade category. 

Glad you got it figured out. I know its a pain in the butt!