The term "incidence" generally refers to the difference in the angle of the wing relative to the horizontal stabilizer. Draw a line through the middle of the wing, and the middle of the tail. The difference in these lines is incidence. For a flat bottom wing, the bottom of the wing would be OK. For a symmetric wing, the line is straight through the chord of the wing.
Quite often the airplane designer will also show an arbitrary line down the fuselage and show various angles of "incidence" from that line. For example, the engine thrust may have negative and/or right incidence as compared to that line. Usually the horizontal stab is parallel to that line, and the wing may have a few degrees of "positive incidence", meaning that the wing angle of attack is higher than the horizontal stab