Natures Miracle is good for getting rid of the smell.
For us, we had to steam clean the room (prof.) to make it all better. We had used the at home units and they just don't do it as good as a hot prof. one.
Going to the bathroom in the crate is different than on carpet.. the crate should be seen as a den and they should NEVER go in there den.
If they are you should make sure they go to the bathroom before you put them in, or completely clean the crate.
Remember not to use a crate as punishment but only a place to sleep at night and go when you are not at home.
Good luck, our 9/mo is pretty much poddy trained 100% but if he drinks to much and we forget to take him out he will tinkle on our wood entry way and let us know LET ME OUT.
I sure he would bark when he had to go