Most marking in a rescue resloves with in a short period, after their smell is around the home and the pecking order has been established, which may still be occuring between the BC and your new family member. creating is important, even in the day, and I suggest getting rid of the soft sided creat for a proper veri-kennel or wire create, one he wont beable to just, unzip. this will help the escapes, espically a wire create that you can, if have to, lock shut in a couple different ways. make sure the create is small enough to discourage the peeing.
Make sure the territory marked is covered with another scent, we use viniger and pepper and sprits the area. Try rubbing the new dog with a towel and then rubbing it over different pieces of furnature in the house to let him feel more secure with his scent being around. Yes you and your son need to be the higher rank, but your BC and the new dog have to decide on their own who is th ehigher ranking between the two of them, there may be arguments and some marking, the best thing to do to make the transition faster is, don't break up the fights, just watch to make sure no blood is spilt, and make sure which ever dog backs down, that you treat as the lowest ranking, pet him second, feed him second, everything, even if the second is your BC, other wise you the issues your having will just get worse over time, not better.
Good luck, and thank you for helping out those dogs abandoned by sociaty, its great to know both your dogs are rescues.
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