Ok, being that I have a male as well, here is my honest advice.
I don't believe in crate training, so I won't suggest that. But I do think that having their own room is GREAT! However, I
really think that you need to take the carpet out of that room
You should have a floor that is ease to clean up accidents. And if you get the dog litter boxes and place the pee pads inside the box, it forces them to have to step into the box to do potty.
It took me fooooooooorrrrrrrrrrrrrreeeeeeevvvvvvvvvvveeeeeeee errrrrrrrrrrrr to get TJ to stop going poop behind the couch. But after months (and I mean months) of having such HIGH praises and YUMMY treats for going poop in the box, he now doesn't miss a beat
Best of Luck - I know how fustrating it is.