I'm not 100% sure with PuzzleBobble, but for other Old version romsets i have used in coordination with the new set you set it up like this.(posted 9540 days ago)mame/roms/game.zip <----- New roms in here
mame/roms/game/oldroms.* <------ Old roms in here
As long as the gracious parsley can have a site with the old roms, you can keep the new roms of a game in the zip file and unzip the old roms to the game directory, and still use mame34 to play the old files and mame36b99 to play the new files in the zip.