Regarding upthrust - I try to set up all my original design bipes at very close to 0-0-0. (Zero thrust offsets, zero wing incidence, zero horizontal stab incidence) About a half degree of negative incidence in the upper wing may help aerobatic line holding, particularly if the wings are positively staggered. BMatthews' comments on stagger are entirely correct - stagger is structurally inconvenient and tends to increase weight, and does very little to reduce induced drag, within the normal range of stagger. The actual numbers: wing tunnel tests revealed that three inches of stagger are equal to about one inch of additional gap in reducing induced drag.
Positive stagger (upper wing ahead of lower) was found to give a slightly softer stall in wind tunnel testing.

Upthrust might be required with a bipe with an unusually high thrust line, in combination with very fat, draggy tires, which could place the center of drag significantly below the thrust line, something I have not as yet encountered.