Yes, Kymaera can support lists of games from multiple emulators, it's still somewhat un-documented, but here's how:
This feature was intended on being used in conjuction with a "Favorites" list.
1)For every emulator, when you set up a gamelist, click the "Set games in Dest. to current emulator", then save your list back out. This sets all games lin the list to the current emu.
2) Create an empty list named "favorites.xml" by going to the game catagory list creation dialog and clicking on "Save destination games list" button and typing "favorites.xml"
3) Add the favorites list to one of your emulator configurations.
4) Go to the "Inputs Config" screen and make sure you've got keys set for "Add to favorites" , "Next Catagory", and "Next Emu"
5) At this point, everything should be set up. Run Kymaera, and you should be able to add games to the favorites list from any emulator. You can get to the favorites list by going to that emulator you put it under and using the "next catagory" buton. All the artwork and launcher settings are then used for each specific game.
Let me know if you have any problems or need any clarification.
-PMF