The PC floppy controller is not able to handle Amiga floppy disks, no matter what kind of drive is connected.
There are several hardware and one software hack available which allow to *read* Amiga floppy disks with standard PC hardware, but none to *write* them.
The only way to write Amiga floppy disks is the Catweasel controller. With this special controller you can read and write Amiga disks on a standard PC floppy drive.
http://www.ami.gaThe "Add PC drives at startup" option in WinUAE is to add the PC HDD partitions as Amiga partitions to the emulation. It does not allow low-level access to these drives.
Bye,
Thomas