Here is a very good stepwise process to crate training. I think Andrea is right and you may have to take some steps back to make some forward progress.
http://www.dragonflyllama.com/%20DOGS/Levels/LevelBehaviours/TL3Crate.html
What I meant by not willing to just accept it was that I want to help make it better… not just say ok, he pees in the crate. That's all. He is doing really really well. And he is fine during the day when we leave him- no peeing or any destruction of his fleece blanket that he's laying on. So that's good. I think Gary got it right with giving him something to keep him occupied longer-- some type of non-stinky chew. We got him a new bed today and they are doing really well on the leash splitter we got. We have even gone down to just one food bowl without ANY aggression at all!! 
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Just out of curosity...why one food bowl? Some of my clients do this, and I just don't understand why. You can't tell who is eating what, or when, and you give away the control of being the one that controls the food. I just don't get it!
Glad to hear things are going well.
Oh Andrea… Always playing devil's advocate...
I prefer to have one food bowl for my dogs. It's just a preference. My longtime dog is used to 1 bowl no matter how many dogs. And she free feeds. We went to 2 bowls when we added our rescue, Miles, and it actually seemed to promote more aggression in our home. And that's just for our situation. Lexi seemed to go, "Wait, where's my food?!" when it wasn't on the floor all the time. And Miles was just hungry. So trying to put food down was nearly impossible without them getting into a spat saying, "Get in line buddy, I've got first dibbs on these bowls!!" It was always a very frantic and overly excited time when things could go wrong- they drew blood twice the first week.
So for us, once the two dogs got used to each other, it's worked well to have just one larger bowl. They can both free feed without over-doing it. And they take their turns which I personally feel helps with the rank structure here in the house. Everyone is very respectful of everyone else. Plus they were making a HUGE mess when we had 2 bowls. They'd run and drop food all over the carpet and also all in between the bowls as they'd check each others' dishes out to make sure the other didn't have something better. With one bowl they aren't doing that. It just works for us.
We pay attention to who is eating and when, but you're right, we don't know how much each dog is eating. But we do know that both dogs are eating and that's what we need right now. If one's weight started to drop off, or if we noticed one wasn't going to the dish as much, we could do something. But I personally don't think the putting the food dish on the floor is the only way to have control in the house. Besides, they still watch us put the food in the bowl. They know that we are the ones that give them food.
Our dogs are our kids. And we pay attention to them unlike pets, but rather like our sweet babies. We know them and their habits (getting to know Miles still obviously) and are very aware with something small is off. Having one bowl just works for us. Not everyone will have the same situation. You gotta do what works for you.
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Just trying to help people one B at a time 
We just always feed our dogs in their crates. Helps them have a nice feeling about their crate; and keeps the pandemonium to a minimum. As you said, do what works for you, I was just trying to hear why other people like to do it your way. I haven't met one dog trainer or vet yet that advocates free feeding for dogs, or feeding multiple dogs together, but of course, as you mentioned, your dogs, your choice. I hope it keeps working for you.
We just always feed our dogs in their crates. Helps them have a nice feeling about their crate; and keeps the pandemonium to a minimum.
We used to feed ours scattered around the kitchen. One fight and a trip to the Vet, a $300.00 Vet bill…..we feed in crates now.:)
It is of course is a personal choice and whatever works for you! We probably all do things just a little different.:)
Okay… so last night we put the kids in their crates and Miles had his reflexive pee thing happen again. It's almost like he was traumatized as a puppy and when he goes in a crate, he pees. He definitely doesn't need to go and he's not really frantic when he gets in either. I mean, he doesn't like it, but he's stopped trying to open the door and stuff. Now he just goes in very eagerly, waits for his treat and then starts turning in circles and then pees. I think having the peanutbuttered hoof in there has stopped him from doing this, but he didn't get it last night because he had chewed too much the day before and got sick. Anyways... thoughts on this peeing?? I still think the hoof in there might keep him from peeing even if it doesn't keep him from howling.
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Weird! Does he always turn in circles when he goes in, or only when he is peeing?
So, for the most part, he isn't doing it as much, but will still, if he doesn't have the chewie thing? It could be just be a set back….or it could be directly linked to not being distracted by the chewie. Can you try different exciting enrichment, so that he always has something, but doesn't overdo it on one thing? On the Kong list someone posted a link to Kong recipes...maybe he would like one of those? I know lots of people (including me) have said that their dog doesn't dig Kongs...but if you really stuff them with the right treats, it can make all the difference.
I think you are doing great work! What a contientious (sp?) B mom!_
If the hoof is present, he'll sit down and chew/lick. If not, he sometimes sits down. Other times he turns in circles and then pees. And then it's like he feels bad or embarrassed or something and tries to lick it up as fast as he can. Makes me sad. I think I will take a look at the Kong recipes though…
Sometimes peeing while turning in a circle is a form of territory marking. It does sound like as he gets more comfortable with the situation, this behavior will stop.
