Currently, I only know the manual way, I havn't seen any automatic ways yet..but now I'll be searching, you can be sure of that, hahahaha. Anyway, I'm guessing bullet and Chirone answered your question but just in case it's not what you meant...I'm assuming you are selecting the whole model and then doing the auto unwrap thingy. If so, I'm thinking you could just select the faces of the parts of the model you want, then unwrap. That way it only unwraps the part of the model that you had selected. Then select the faces of another part of the model and repeat, etc. I don't know what unwrapping is yet, but it seems like it should be able to work that way.