Jim,
Generally a reference of incidence is the angle between the cord line of the wing where the wing is mounted to the fuselage, and a reference axis along the fuselage longitudinal axis, so If your fuselage is positioned longitudinally to 0 degrees and you set and lock your your wing to lets say 2 degrees positive while your fuse is locked at 0 then this would be a 2 degrees positive A of I and vise versa for a negative A of I setup. The same applies for a canard or a horizontal stabilizer. On most all of my stuff I set all my incidence to 0 degrees from one another, wings fuse, and horizontal stabs. I hope this is useful information to you.
Bob