[Yorkiex]

I've had baby Leo for a few months now. He usually does pretty well on the pee pee pads only peeing and pooping on those but sometimes he misses. I have a custom kennel for them that I had made and so their beds are unconventional. It's pretty much a gigantic full body pillow with a waterproof cover and then a cuddle cover on top of that. The smell of his urine when he misses stays on there and NOTHING but bleach and laundry detergent will take the smell out of the waterproof cover. He now automatically associates the corner of the cage where his pee pee pad usually goes with the bathroom so he'll pee and poop in that spot regardless of there being a pad there or not.
I recently started to crate train him at 7 months old. Not sure if it's too late now and I'm just going to have to take him out a million times a day and get him on a schedule to potty train him. The problem we were faced with last night was un-ending whining. He was barking and whining and howling ALL NIGHT LONG. I barely slept a wink because of him. He didn't stop until we moved one of our other dogs in there with him and finally got about an hour of sleep. Is there any pointers anyone has for someone in a situation like I am? I'm tired of the cage smelling like pee and I'm not sure what else I can do to make sure he doesnt cry at night.