I highly recommend crate training for dogs, it seems to be comforting for the dog to not have much space to worry about, and there is less for you to worry about leaving them home alone. Once they are also potty trained, chew trained, etc, you can leave the door open on the crate and they will go in there on their own to sleep or relax. After a while we moved the crate to the garage and the dog found other spots to sleep. Ours has at least 7 "favorite" spots to lounge (one in a corner under a table, her new "crate"), and we have beds in three different spots for her. It might make less of a difference with a puppy, but for a rescue who comes with bad habits I think it's great.
I also think Cesar Milan is worth watching/reading. He has a TV show The Dog Whisperer, and I've really learned a lot about why dogs do what they do and how easily they can be trained.