So lets clarify, what are you trying to do exactly? Just make the disks work on amiga, or try to make both amiga and pc read the same floppies so you can transfer files over?
If you want to transfer the files over: Format the disk 720KB (if the floppies are HD ones, you need to tape over the extra hole). Then on Amiga you must move Devs/Storage/DosDrivers/PC0 to Devs/DosDrivers and reboot. After this the amiga can read PC 720KB floppies.