Both Sephira and Ninja_Jackie_san bring forward excellent points. I'd like to expound a little on both. Sephira mentioned the extent of the difference in size. This is a pertinant point. If one is swollen, there is a problem. Another thought is, you are stronger on one side than the other and your muscles may be more developed. The sac is big enough for both. Your personal comfort on how they arrange themselves is dictated by how they droppped, your personal sleeping habits, and how you wear them in your underwear while you are maturing. Ninja_Jackie_san brings another very good point to ease your concern. They do hang lower when you are warm. This also goes back to placement. When you are sitting with your feet flat on the ground, your legs are close to one another. One is going to slide in front of the other. This is normal. It shows your biological "being" is doing all the right things to encourage semen growth and health. They don't like being too hot or too cold. Almost all males of any mammal I've known have one bigger and lower than the other.
It's actually very common. No one (guys or girls) is completely symmetrical, so there is always one side of our body that is bigger/smaller than the other. The only time it's really any cause for concern is if it's a major difference, but in those cases you can talk to your doctor and they can check it all out for you.
The saddest thing is that some people undertake expensive procedures to correct what they perceive to be an abnormal "misalignment". Women seeking "repair" to their differing labia are far more common. It's really unfortunate.
Blame it all on our perceptual concepts of beauty focusing on symmetry...