I am going to actually base it on which side of the 2D plane the unit is on since the rectangle you see on screen maps to a warped quad in 3D and some units are being selected that the user wouldn't expect. That's also a very simple change to make which is just testing the distance of the x of the unit in comparison to the plane definining the two sides of the selection rectangle. This will give the exact results that I want and is a very easy feature to implement which I will do sometime.
As you can see, each unit that is selected has it's bounding box turned on. I also add it to a list of currently selected objects which I can use later if need be. It'll be used in things like navigation for when the user right clicks to move a group somewhere, etc. I think I may start work on getting a unit to navigate around the terrain which will be a very important feature.
Progress has slowed a lot due to midterms but once they are over, I plan on getting 100% back into development. It's been steady progress when I've had time. I'm still on track with my goals as well so that's always a morale booster.
Screenshot: 1280x768x32 - No AA - Default ATI Settings