As I recall from a long time back, the incidence is measured against a fuselage reference line. Most full scales set this line so the fuselage is in an attitude of least drag, or the attitude they want the plane to crusise at.

In RC monoplance we normally use a 0-0-0 set up. This is wing, stab and engine all at zero degrees. Some biplanes and others use positive incidence, but sport and acro planes mostly use 0-0-0.

Robart used to sell a very inexpensive incidence meter. I still use the one I bought 20 years ago.

My procedure is to put a level on the stab (if it's flat) and prop the fuselage so the bubble centers. If it's an airfoil stab I use the incidence meter. With the fuselage set, I carefully put the wing on and re-check the stab. Then I check the wing incidence at both tips, shimming if necessary. In this position, I also check the angle of the firewall and shim the engine as necessary for either 0 deg. or whatever down or right thrust may be required.

I should say that I also join wings with the meter. It doesn't matter what the root is, most of the rolling force comes from out near the tips. When I join 2 panels, I prop 1 side up and get the incidence at 0. I weigh the wing down with magazines. Then I put the second wing panel in place ahd check it at the tip. If I can get both to 0. I glue them together. Some times the root is off by a good amount (meaning there is a warp in the wing.). It's the tips that count.