Hi, pbandj. Welcome to the board.
Your puppy is still a baby and needs to be taught what to do. That means that for a while you'll have to invest some training time with him until he learns what's proper for him to do. Although he can let himself out, he doesn't really 'get' that the house is not for peeing, yet. He doesn't know he's done wrong--he just knows that you're upset without really understanding why.
For pups of his age, you need to set up a schedule. Take him out (not just allow him to let himself out, but go out with him) right after he gets up, after he eats, before and after a play session in the house, last thing at night and any time you see him giving signals that he has to go. Sometimes those signals are very subtle and hard to spot, but if you watch him closely you'll start to pick them up.
When he eliminates properly outside, quietly praise him and tell him he's a very good boy!
He'll catch on, but it can take a few months. Patience and consistency are your best allies while training.
If you have trouble keeping up with him in the house, you may also find tethering useful. Attach a short leash to your belt and use it to keep him at your side during the day while you're at home. It'll not only help you pick up on his "I gotta go" signals, but also teach him to look to you for direction.