Just and Idea, and I have done this with easy success, select the faces you want to UV at one time, and automap them. In your UV editor, simply sew everything together. Do that or all areas of your model. This way you wont have to worry about a huge mess to figure out out to put together. All your doing is working with one side at a time.

Here is an exmple of a cube I auto mapped from one side. I just selected all the faces on that one side and simply automapped it.