I had the same problem with multipart files solved it by editing the 'use custom command line parameters' in the emulation tab of each game.
 
	To get Centipede running I used this
 
	-cart2 "C:\Commodore VIC20\Centipede2000.crt" -cartA "C:\Commodore VIC20\CentipedeA000.crt"
 
	Thanks  MacGuyver your tips helped me when I was about to give up.