Ok all this is all just my opinion but I wanted to put it out there bc my mind hadn't even gone this way until earlier today. I had an idea maybe they really were separated but Sc was still in the kids lives, he offers to give Bernadettte a ride somewhere, or they go off to do some photography thing or something. He then tells Bernadette he's not really their father, and tries to make a move, she reacts and he kills her then proceeds to create the story of how she went missing. He tells Sa him and B got into an argument, she stormed off claiming to be suicidal. He says he was angry and drove off but felt bad turned around to look for her couldn't find her, calls Sa sending her off looking for her, so the night she went missing they both weren't home and both came home with no Bernadette and being gone for hours. Then I have 2 possible scenarios either Sa believed him but at some point realized he was lying and continued to help him hide what he did, Thus both being charged with murder. Or maybe he told her he killed her she was the one to turn him in and he's flipped it on her and placed her at the scene with them and she has no proof she wasn't but GPS shows them both out that night in random areas, especially if something of Bs was found in an area Sa GPS confirmed she went to. It just feels like it makes sense. Idk this is all just my opinion though. I feel it was something along these lines...
My only doubt with this is that I believe Bernadette and her older brother would have known Scott was not their real Dad. She was around 6 when he came into their lives and the brother older than that. Therefore you’d have thought they’d have spent some time with their real Dad.