If you cant disable the controller on the motherboard, then you are screwed.. You always need to disable something to enable the other.. Why not? Because if its still enabled, then it always would assigned the drives first to the controller that is still enabled. So if you would adding an HD controller to that board, that controller wont be available, because your old controller on the boards overrides it.

this is what I suspected unfortunately. I was hoping someone had come up with some kind of work around.

AFAIK older PC systems could support 4 floppy drives (the first one at 0x3F0 and the second one at 0x370), but thinking about it...
- DOS uses A: and B: for floppy disks, and C: for hard disks... if two FDCs are installed, the first hard disk would be E:?
- You will need a floppy controller that can be configured for port 0x3F0. It seems that most of them are hardwired to 0x370 and only allow enabling/disabling FDC port.
- PCs and XTs had the old reliable 765, that don't support HD floppy drives (well, you can connect an HD floppy drive, but it will act as a DD one). I guess that having a better FDC on the floppy controller would enable them to use HD and EHD disks on the third and fourth floppy drives, but I don't know for sure.
- You will still need some bays for your drives.

I remember as a kid doing stupid things like putting an ISA floppy controller card onto machines with onboard FDC and connecting floppy drives to both. They'd both seek at POST since they both get reset at the same time etc. Not a good idea obviously, especially if one throws an error and the other one does not 😉 Not to mention timing issues. Terrible terrible things to do. Hey, you live and you learn...