The 3 configurations are:
A) Conventional takeoff and landing (CTOL). A normal fighter jet, intended to replace the F16.
B) Short takeoff and vertical landing (STOVL). This model essentially has a big fan in it to allow it to hover and land on aircraft carriers.
C) Similar to A, but with larger, foldable wings and a stronger tailhook for landing with a carrier arrestor cable.
Model B is intended for the Marine Corp, and C is intended for the Navy.
Now I admit that I am fairly uninformed about military hardware and design, but I think something can be concluded from the F35 program issues.