Having a good pack structure reduces such problems. The dogs see all the
people and dogs in the household as a pack with each having their own rank in
the pack and a top dog. Life is much easier if the 2 legged pack members
outrank the 4 legged ones. You can learn to play the role of top dog by
reading some books or going to a good obedience class. A good obedience class
or book is about you being top dog, not about rewarding standard commands with
a treat. Start at
http://www.dogsbestfriend.com/. Dogs are not mature until about 3 years old. As they mature, they challenge you for leadership and status. Firmly establishing your status as top dog will help.
Eliminating in the crate is a very effective way of upsetting you and proving you can't control him. You need to reduce the consequences to you. Remove the bedding and replace it with a rack. They are available with the crates, but a piece of closely spaced wire closet shelving from a home supply place is cheaper. Urine goes through the rack and can easily be sponged up. Bowel movements don't work quite as well, but still limit how much of a mess he can make of himself.
Stand your ground. Do all the top dog stuff, eating first, go through the doorway first, reserve the best sleeping places, make him move out of your way, make him sit quietly before opening the door for him or feeding him, etc. Use the rack to reduce the problem. Control your emotions. They are hard to hide form a dog. As his protest is less and less effective, and you show you are top dog, he should give it up before long.
Neuter him if not already. It is no cure all, but does reduce behavior problems. Certainly dogs with behavior problems should not be used as breeding stock. It also reduces chances of cancer in later life.