Stephen , the incidence for both the top and bottom wings are checked in the same manner. You should, have zero incidence between the top, top wing, bottom wing and elevator. I began with the bottom in the wing saddle and then with the fuse propped up to maintain zero incidence on the bottom wing. I then checked the top wing and without changing anything it too should also read zero.

What I was referencing to regarding the top and bottom wing alignment was in reference to how the top wing aligns to the bottom wing, if you were looking down from the top of the wing, and then checked the alignment left to right as the top wing aligns with the bottom wing. This is done in the process of mounting the interplane struts which if not checked will most certainly be off.

Does this make better sense or is it still confusing?