My puppy is 12wks old and he seems to already be making his territory. When I took him to my boyfriend's apartment he kept leaving small piddle spots in the different rooms of the apartment. I was making sure to give him his potty breaks and he was doing most of his piddles outside. The small piddle spots didn't seem to be from not being able to hold his bladder because he would just squat and leave a tinkle here and there. He does that around his poo spots outside too.

Do puppies mark territory? and if so how do I get him to stop?

That's pretty much what puppies do before they get older. Just keep potty training him. Whenever you see him start to sniff around scold him and take him outside.