Well, I use a 4-floppy Compaticard in a P5-A motherboard. I don't use the CC BIOS, but rather the native on-board BIOS. The second two drives on the CC are strictly for use with direct-access utilties such as ImageDisk, 22Disk, etc., so they don't need native BIOS support. I suspect you might get that under DOS using the Tulin driver however.
At any rate, if your board is anything like the P5-A, the trick is to install your floppy controller with its BIOS disabled, but otherwise at the primary floppy address (3Fx). Next, go into your BIOS setup and under one of the menus you should have one that says "Onboard Floppy Controller" or something like that. Set that to "disabled". Leave your primary menu drive A: and B: choices to reflect reality.
The board should boot right up using the BIOS-declared floppy settings, but using your ISA controller. My P5-A is set up this way and runs DOS, Win98SE, Windows XP and Ubuntu with no problems in accessing the floppy drives. As I said, the second two drives are both external and are used by non-BIOS-dependent utilities.