I used to have a Starduster SA-100 (single place), so my recollections are from that design:
Upper wing has slightly higher AOA so starts to stall first while lower wing continues to fly as nose drops a little. In practice, unless stall is accelerated, plane simply mushes while retaining aileron control. Falling leaf w/rudder is a piece of cake.
Distance between upper and lower wing theoretically is as far as is reasonable to minimize interferance drag . . . that was also the logic behind Walter Beech's design.
Haven't seen flaps on upper wings, but when flying the little Starduster, even putting my hands above the windscreen would result in a pitch up, so I suspect upper wing flaps would require significant down trim authority to trim out - - depending on speed it might not be doable - - at least on this particular design.
Also, due to the additional drag, two wings isn't nearly twice the lift of a single wing of the same span. From Wikipedia:
"In a biplane aircraft, two wings are placed one above the other. Both provide part of the lift, although they are not able to produce twice as much lift as a single wing of similar size and shape because the upper and the lower are working on nearly the same portion of the atmosphere. For example, in a wing of aspect ratio 6, and a wing separation distance of one chord length, the biplane configuration can produce about 20 percent more lift than a single wing of the same planform."