Okay, an update for you, I'm using a Commodore monitor for the AGA and an SVGA one for the voodoo, by the way.
Anyway in the settings I have
Prometheus (1) - Village 38 (ID $5002)
Prometheus (1) - Village 38 (ID $5102)
I've tested the modes on both of these, however when I click test, the native display freezes with the busy pointer, the vga monitor flicks, but doesn't chaange screenmode and remains blank.
Robert
Edit: Earlier on today I inserted and re-insterted the prometheus several times, as well as the voodoo to the pci slot.