You'll need to know the correct device and unit numbers of your drives. It sounds like you've got this from the Blizzard SCSI Tools.
Then you'll need to check the file DEVS:DOSDrivers/CD0. There's either a setting in the ToolTypes, or the file itself to change the device and unit. With multiple CD drives, just clone CD0 under a new name and change the unit again.
I think BurnIt doesn't depend on a CDFS, and accesses drives directly via device and unit number (that's how MakeCD works, at least).
If this isn't clear, let me know, I'll try to elaborate.
