Hi,
1. I didn't completely understand your description, but if you can imagine it as a 2D geometry, the easiest way is to calculate the average U, based on the area and U-value of each element: Um = U1A1 + U2A2 / A1 + A2.
However, in advanced levels, we derive this kind of U-Values by modeling two-dimensional heat-transfer effects in tools like LBNL Therml, Antherm.
2. In EnergyPlus, in terms of geometry, you just have surfaces and not thick walls. I don't know why you are concerned about the position of windows. If it's about thermal bridges, EnergyPlus does not take 2D or 3D heat transfer into account. If it is about shading, you may put some extra shading surfaces.
Best,
Farhang