So I bought the Junkyard dog, 200 caps for 5 defense isn't bad, plus, another dog. I sent him to Sanctuary, which is where Dogmeat hangs out when I'm not using him. Since I want to know where the good boy is, I took out all the other doghouses and just put one below my treehouse.
When I cam back home, the Junkyard Dog was in the house, looking up at Dogmeat. The good boy was sitting, with his head tilted, looking a little sad. So I built a second doghouse next to the first one, and the JD casually got up and strolled into the new one, leaving the old stinky one for Dogmeat.
I love this game.