2 yr old Yorkie: separation anxiety, peeing in crate, behavior problems

Question
We were given a 2 yr old male Yorkie on Memorial Day (not neutered).  We already have an 11 yr old female Silky Terrier.  At first he was very leery of being touched and would dance away from your hand, seemed very high strung and anxious which is to be expected in a new environment.

He is peeing all over his crate whenever we put him in it during the day and barks like crazy or whines when he is in it.  We just now put him in the crate for about an hour while we were in the house and he barked non-stop and urinated all over it and himself.  He has urinated in his crate every day after we leave for work.  He doesn't pee when he is in his crate at night though.

He also is still trying to be the alpha and deliberately disobeys us.  He can refuse to come when we call him even though he just did it an hour ago, growl and try to snap back, pull at the leash when we walk him, and whine or bark when he is in his crate.  He seems to be very conflicted, sometimes we can get him to show us his belly, and other times he gets stubborn and tries to "out-alpha" us...

I don't know what to do or where to start with him, I have read a lot of training guides, but they don't seem to be making much of a dent so far.

Answer
Peeing in the crate is abnormal behavior and can be a symptom of severe psychological issues. I suggest you get a trainer. Betterdog.com has many locations and quality trainers, so check them out.

First, get him neutered. The last thing he needs is hormones messing with him on top of everything else.
Next, check out this article to make sure you're doing everything you can to be a good pack leader. http://www.thegooddogjournal.com/2009/02/whos-boss-establishing-pack-leadership....
Then check out this article http://www.thegooddogjournal.com/2008/11/separation-anxiety.html to make sure you're doing everything you can to help ease his separation anxiety.

Those are starts. This will take some time and you'll need to be patient. A professional trainer will be very helpful to you if you can manage it.