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.