I would really start working with him on the crate issue. He most likely will pitch a fit in there the first few if not several times. That's normal and to be expected from most dogs. Just ignore his barking and whining and he will eventually give it up settle down. Don't let him out until he has been quite for a good 2 minutes. If you let him out during his fit, he will quickly learn that all he has to do is bark and cry and he will be let out. You can also practice by crating him for short periods of time and let him out after he has stopped barking. Once you repeat this a few times, he should get the hang of it fairly quickly. Just don't give up on it and be consistent. Also, make the crate a fun place by putting a couple of toys in there. You could also toss a Kong with frozen peanut butter in there to keep him busy and quiet for a while. Crate training really is the best method. I couldn't imagine getting by without it.