The fuselage is just there to hold the tail and wings. Incidence measurements relative to it are meaningless unless it easier that way and subtract the two. You measure the full flying tail relative to the wing. Set it at a couple of degrees negative initially and fly it. Adjust as required because with a full flying tail the incidence is defined only at the time you have your hand off the stick.

Stability and penetration are more a issue of CG location and weight. Move the CG forward to get stability, add some weight for penetration. There is more to it that that of course but it is a start.

A full flying tail with several degrees of negative incidence and a forward CG will have a strong angle of attack stability tendency. Move the CG aft and the incidence will go toward 0. Get one of the lazer incidence measurng devices.

The fuselage is just there to hold the tail and wings. Incidence measurements relative to it are meaningless unless it easier that way. The aero of the airplane cares about tail relative to the wing.