There are really three things to be concerned about here.
The first is the boot drive. The Apple II scans for a bootable device starting at slot 7 and working towards slot 0. From my recollections, it doesn't matter which slot the bootable device is in, though you'd probably want to put a hard drive in a higher slot and a RAM card in a lower numbered slot, with the floppy drive controller inbetween. (Quite often, RAM cards would look like disk controllers since the Apple II could only address 48k or 64k without bank switching.) Of course you can change the boot order with a special boot loader, or typing something like "PR#3" (where 3 is replaced with the slot number) at the BASIC prompt. If you're dumped into the machine language monitor, you would type something like "3^P" where "^P" is control-P. (No quotes in either case.)
The second thing to be concerned about is the matter of using a IIgs. The Apple II was originally designed to address eight additional devices. The IIgs couldn't really break compatiblity with the II, so it couldn't alter how the keyboard, display, joystick, speaker, or tape drive appeared to 8-bit software. It couldn't simply add devices either (because that would mess up the memory map), unless they appeared to be on a slot. Apple got around this by adding peripherals that were meant to be seen by 8-bit software to soft-expansion slots. In essence, the firmware would redirect requests for a certain slot somewhere else. This was fine for the Apple IIc because you didn't have any physical expansion slots, but it wouldn't work out for the IIgs. So Apple added additional functionality to the IIgs firmware that would allow you to put "My Card" into a slot, while disabling an expansion slot's function.
But once you consider those two things, it doesn't matter where you install a floppy controller. Well, unless you are using a particularly poorly written application. In most cases, it probably won't matter at all since I think it uses the default disk controller to save data (i.e. the one it booted from). In other cases, it will allow you to specify the slot and drive number. I don't think that ProDOS programs care at all, since they usually deal with paths and let the OS handle the rest.