So, I went through this same thing with my Dane when he was a puppy and I forgot how nasty it is! When my dane was a pup I would crate him and he would throw a fit ALL night and in the morning he would have pooped in his cage and stepped in it and it was everywhere!!! I attributed this to part social anxiety and part possible dirty breeding conditions. This all stopped as soon as I let him start sleeping in my bed...then he was perfectly fine, but still has a bit of social anxiety in him (but not destructive thank goodness).
Well now with Spyke, he seems to act the same way in his pen and for whatever reason, he refuses to poop in his Rascal Dog or on pee pads in general. He cries as soon as I'm out of site and all night long while in pen. However, I have been leaving him in his pen for a couple hours the first night and a few the next night and then I get up and play with him a bit and we usually end up falling asleep in my bed and he will find a corner of the bed to lay in and sleep all night. Anyways, I have no problem leaving him in his pen, but I figured since he's only been with me for a few nights now I'd work him up a few more hours each night. Next week I will be back to work 3rd shift and he will be in his pen while I'm working.
Sorry, I'm rambling...my biggest problem is that he will refuse to poop on pee pads & Rascal Dog, so he poops right next to the thing and then stomps all over it and it gets all in his paws and all over the floor. I came home from a short hour trip to WalMart and it took me probably an hour to clean up the mess. He had poop everywhere in his pen and it was caked all over his paws. I just threw him in the tub with about 2 inches of water and started to clean up the mess and he somehow managed to get out of the tub and I look behind me and there goes Spyke hauling ass down the hallway! LOL I'm just not sure how to even approach this....like I said, my dane outgrew it, but I remember every morning having to drag his crate outside and hose it down while cussing up a storm and cleaning him off. I really don't want to have to do that every morning I get home from work....
Yes, I have tried taking a turd or two and putting it on the pee pad so he know that is where it belongs. My house is always kept clean and the breeders house was VERY clean also...
Any advice???

How big is his pen? Others are probably more qualified to answer, but can you reduce the size of his pen so it is only as big as his sleeping area and potty area. Spyke should not poop or pee where he sleeps, so if the pen only has room for a small sleep area, and the Rascal Dog, then he should use the Rascal Dog.

I don't know. Buddha cried and howled the first night. I already knew that I didn't want him sleeping in my bed so I put earplugs in and let it go. The next morning he was so precious. I went down stairs and he was still whining so I opened the door to his crate but he wouldn't come out. He just kept whining with the door open. So I made coffee and sat down in front of his crate and tried for 15 minutes to coax him out. I finally reached in and got him. The second night he did a little better he cried but I didn't take him out or attend to him in the night. He did come right out the second morning. The second day I started telling him "no whine" when he whined In his crate. I only had to tell him twice.

Buddha never liked pee pads. I bought some because it was getting cold outside and I didn't want to go out but it was worse waiting for him to figure out what to do on a pee pad then it was to take him outside in the cold and get it done.

Also I still time Buddhas food and potty needs. I try to make sure that he is as empty as can be before I crate him for bed.

Good advice, but yes I try to time him too. While working 3rds he will be in his pen all night whether he likes it or not...and I won't be home to hear him whining and crying. He doesn't poop or pee where he sleeps. He has a crate inside his pen. Basically he has enough room for a couple toys, water bottle, and Rascal Dog. I have a few pee pads set up outside of his pen, around the house, and he won't poop on those either. So I've caught him mid-poop a couple times and he is looking at me like "what the hell" while I'm running with him over to the pad while he is mid-business.... I guess the thing that most concerns me is that he is okay with stomping on his poop ... or maybe he isn't.... I don't know...

Well to me it seems like he might be confused. Why so many potty options?

I only have 2. One in his pen and a pad at the other end of the house in the mud room

Sorry, that was confusing. The first night I did have a pad in the living room for him since he didn't know the house well. He only has 2 now

I don't know. Sounds like you gave him free reign. Potty can be tricky I would stick to one option and I personally wouldn't create a yard in the house.

When we got our puppy this is what our breeder told us to do:

- put him in the crate at night with a cover on it
- have a two hour window for crying - so for example if he went to bed at 10, ignore the crying until 12. If he cries at 12, let him out, no attention, no talking, no playing, no eye contact, just put him on the pee pad (I had to sort of corral him with my feet to keep him focused on the pee pad). Wait until he goes, and make sure he has sufficient time to do both activities if he needs to. Once this has happened, or enough time has passed that you know he isnt going to do anything else, put him back in the crate. Ignore all crying for at least another two hours. Repeat if necessary. I did not treat or praise my dog during the night (although I did praise him for going during the day, no treats though, I didnt want to start up with that)
- make sure crate is small enough that he wont go to the bathroom in it (no crate pads). We used an airline style crate and put a box in it (I think we only needed the box for a week or so).
- the first couple of weeks are the hardest, it does get better!!! That's why there are so many people who post on here and then never post again!