This is just what I've picked up over the years but I always use total wing area including any hidden by fuselage and nacelles, measured flat (as built ). Effectively you have to do it that way for many modern aircraft because it's almost impossible to tell where the wing ends and fuse begins.

However large the plane it's not normally going to make a significant percentage difference.

A trickier question is whether to include the tail area or not (I don't).

Steve