To use disks for transferring data from atari to pc and vice versa they have to either be double density disks, or they have to be high density with a piece of sticky tape stuck over the detection hole.
If you are using TOS 1.06 or higher then the standard format on the desktop should be PC compatible. if you havnt got this then youll have to use a PC formating utility. Ill send you one if you need it.