The police and FBI knew it was him right from the off. The bed was stripped and the flat sheet was in the kitchen bin, with a matching fitted sheet left at the site he disposed of them. They'd already sent a drone over there because they could see from his GPS that's where he'd been and they saw the sheet and also an area of earth that had been disturbed. They knew very early on that it was a body search.
Even the fact he made them wait for him to gain entry to the house. If there's a suspicion that she might be passed out inside you'd surely instruct them to bust the door down? He was also inside the house for over a minute before opening the door to let them in. No idea what he was doing in there because he certainly didn't cover his tracks.
He definitely didn't think the alarm would be raised so soon. What a great friend Shannan had. Did he not know she had a prenatal check up that day?
He's given more detail since his incarceration, like how he smothered the children before killing Shannan but they "woke up" which made him angry. And he knew when he tucked them in the night before that it would be the last time he did that. He's said that he killed Shannan as she was drifting off to sleep, so not in the heat of an argument as he previously stated. He made plans over text with his co worker to be at that site alone on the morning of the 13th, telling his co-worker not to bother going. Completely premeditated.
I can't get the case out of my head. It's terrifying that a seemingly normal man with no previous issues with violence or anger could do something like that.
If you're interesting in watching more there are three episodes on the JCS Criminal Psychology YouTube channel. He explains some of the psychological tactics used by the FBI agents and it's quite interesting.