Unless you install it on edge or upside down, the
lower head is #0, and
the upper head is #1 (or #1/#2, A/B, front/back, . . . )
For a 3.5" drive it's safe to say that the side where the motor spindle
engages with the disk is the head 0 side. That's normally true of other
sizes of floppy disks too, but with those it's technically possible for
the motor spindle to be on either side of the media, with the 3.5" it
isn't.
-tony