Since he hasn't been allowed upstairs much before, he doesn't know that the rules are the same upstairs as downstairs. It might sound kind of silly, but dogs don't generalize very well (even our gifted Bs!).
Treat his upstairs visits like potty training all over again. Only let him upstairs AFTER you've seen him pee outside. And since the girls aren't able to keep their eyes on him at all times, keep him tethered to you on visits upstairs. That way you can watch for any signals of marking, and he'll likely be paying more attention to you than all the new stuff. After this is successful for a while, he can go up with you as long as you can keep an eye on him. You might even consider adding a "permission" word to let him know when its okay to go upstairs.