I'm not an expert by any means, but sounds like your Joey is marking. When you catch him, clap your hands and give him a quick "no." I stayed in a hotel recently with my boy who has never marked inside and I saw him lift his leg at a wall -- he didn't pee when I gave him a sharp no. Haven't had any problems since.
Make sure you praise Joey and your girl when they potty in the correct place, either on the pad or outside. Never ever stop praising.
Hopefully some of the breeders can give you more advice or information about the effect puppies have on behavior of the adults.
As for your couch, test a spot with a solution of white vinegar and hot water. A steam upholstery cleaner would probably be best. |