@natemac This is what I do, but you need to at least make the choice once. The easiest way to do it is to pick a default, say, lr-mame2003, then go through your ROMs and launch the ones you want to run using FBA and invoke the menu on those, choose FBA for "this ROM" and it will remember your choice.
For me, I have most games launching with 2003, vector games launching with AdvancedMAME1.4, and a handful (NeoGeo, fighters and a few others) launching FBA.
With everything setup the way you want, you can disable the runcommand menu from appearing and a typical user won't even know they are running different emulators.
I don't know a way to pre-select them. They get tracked in a file using some long ID, but by the time you figure out how to use that across each ROM, it would have been faster to just launch each one once.