Hmmm... It should be working with a basic 3.1 install. The built in CD drivers are crap, but they do work. Make sure CDFileSystem is in L: and check the CD0 tooltypes to make sure they're set correctly. If there's nothing there, edit the CD0 file itself to change the device and unit numbers. You'll want scsi.device unit 1. Also, are your master/slave jumpers on the drives themselves set properly?
You should try to replace the CDFS with something else ASAP, though. Try AmiCDFS on Aminet.