Muscle memory. You've been so used to going to the restroom in a sitting or standing position (depending on gender) that your mind and muscles have become accustomed to that position(s). Just keep practicing and eventually you will figure it out.
I still have trouble with it myself but I have found a few things that do help it along. First, relaxation is key to it. You can't do the deed if your all tense about everything. Try playing some type of music that relaxes you. For me, its either sounds a rainshower or ocean waves.
Also something else that may help is to practice in your bathtub. This is one out of the "12 Month Program" that has worked for me. Get a large bottle of water and lay down in your tub without any clothes on. If you can stretch out all the way or for the most part is ideal. Drink your bottle of water and eventually you will get the urge to use the bathroom. Just lay there and try different positions until you find one that works and keep practicing at it. If you practice this every time your in the tub eventually you will be able to transfer the idea from your tub to the bedroom. Practice, Practice, Practice!
I think it took me about 2 or 3 weeks before I became relaxed enough that I could go laying on my back in bed. As for on my stomach, I haven't gave it a try yet.