Black tank Overflowed? How is the best way to clean-up

Well we are not sure what happened. We think we might have let the black tank go too long before dumping. We noticed a odor and the Wife told me to dump the tank, which I did. Later she said it was still smelling and something was wrong. We found out the underneath storage carpet and wood was wet and had the same bad smell. There was no signs of water on the ground or around any of the drain pipe from the toilet. I'm thinking the water must have come from beneath and uo to get the floor wet. Not sure exactly how the connections are made to the top of the tank and if or where the water would come out if overfilled.

Now we still have the bad odor coming in seeping up through the storage area into the trailer. Some questions I have are about the cleanup to get rid of the smell. Will I have to cut out the carpet in the storage compartment and replace? What would be the best thing to spay on the wood to eliminate the odor?
My tanks are enclosed in a covered under belly so I can't see anything. Should I be concerned if something is has come loose or broke? Or is the common on overfilled tanks?

Any recommendations are welcome.