Shannon, there is a lot going on around you, especially with a new baby due
My son is the same age and one thing I've noticed is they're in a very transitional time. Not yet a full blown teen and definately not a kid anymore. I do remember being 12 -14 and I have to say, it was the most confusing time of my life. Do take some time to sit with him and talk, not just about this, but about life how he's feeling about school, friendships and the new baby.
You mentioned that he's feeling that he has little control over things. I think you hit on something very important and as his mother, I bet your right. Are their things he can do around the house to be more helpful and in control - not chores, but things that would make him feel like a more 'grown up' member of the family. Ask for his help in planning the weekly meals (maybe have him write down some meal choices). Have him plan a day outing and give him a few suggestions like zoo, art museum, nature center. See what he's interested in and let him plan it all (you may have to give him a budget).
Lastly, do talk to him about his peeing, you saw that asking him why only puts him on the defense, so try asking him if he could try to hit the bathroom next time because it's really hard on you when you come in to find pee on the carpet, explain how it soaks into the floor and makes things very unsanitary and that you're concerned for his heath.
Another poster mentioned errection, this could very well be a part of the problem and may be worth discussing.
Now, there have been some posts here that have trailed off the original posted topic, let's try to keep in mind the OP's issue and try to offer her some supportive suggestions. I really hope we can keep this about the OP and her issues and take any personal issues to PM