When calculating the lift coefficient, what area is used?
Reference area for the aerodynamic coefficients (lift, drag, moment) is the planform area. Your picture shows only one wing, while the reference area S would also take into account the fuselage and the other wing: orange times twice blue and then some.

In its most generic case, the equation for wing area S is $$\int_{-b/2}^{b/2} c \cdot dy$$ with b = wing span = distance between the wing tips, c = local wing chord (orange line), y is the coordinate in direction $Y_m$.



For clarity in reference, the picture above from my old uni book by prof. Gerlach on stability &amp; control, which shows how the definition works when sweepback and dihedral angles must be accounted for. Note how the wing/fuselage intersection is defined for the reference wing area, by extending the local leading/trailing edges of the wings.