Chad,
The biggest thing that you will notice by chopping off one wing bay on each side is that the plane has a better roll rate. Otherwise you shouldn't notice much difference by doing that.

I think that you're going to find that covering scheme very difficult to use right now. When it comes to determining top from bottom you need to have something that can immediately indicate to your brain which is which. Normally this is accomplished by either contrasting colors or different geometric shapes. Unfortunately what you posted doesn't really do either. Looking at them there just isn't anything to set them apart from each other. As you gain more experience you start to learn to "keep track" in the back of your head. For example, when you roll your brain/instinct "knows" that the plane is upside down. You keep a mental track of how your plane is oriented. But even then you still will have times that you lose orientation. When that happens you usually don't have more than a second or two to determine how your plane is oriented, and that's where you need something you brain can key on to figure it out. As you gain more experience it usually takes less and less for you be able to do this. If I can make a recommendation, I'd say do the top of the wing one color and the bottom another color.

Hope this helps.

Ken