Sky Shark:

You can do the incidence two ways. You should set the chord line of the wing 1-2 degrees positive to the top of the floats. As Wine said, the chord line is a line passing through the center of the leading edge and center of the trailing edge. An easier way, which will give essentially the same result is to just make the flat bottom of the wing parallel to the top of the floats.

I see two things in the pictures that may be a problem. 1- To keep the prop from sucking up water, you want a couple of inches of clearance between the bottom of the propellor arch and the top of the floats. It looks like your floats are too close to the fuselage. 2- As Wine also noted, to keep the airplane from blowing over during crosswind turns, the distance between the floats should be about 25% of the wingspan. Your floats appear to be too close together.

I realize that the way you have it set up looks more scale, but what works for full scale often doesn't work for models.

Good luck with your Super Cub. Float flying is great fun.

Jim