he's peed in the box and lays in it.
That is sign of stress, because he is left alone. Separation anxiety, not the potty issue. He is streessed and it doesn't matter for him where he lays. Actually, it is similar with people - depressed children pee in their bed and then sleep on the mat on the floor, pee on the mat and go back into already dry bed. They do it because their single parent has left them for a month, he is a trucker, asked old neighbour to feed the child, and that one comes twice a day. I'd like to suggest finding a puppy-sitter, not to put the whole issue onto your mom. Your young dog must be active, have company during the day, because he is developing not only physically, but mentally as well.