Welcome to YT!!!
Personally, I could be completely wrong on this but I don't think a 12 week old yorkie marks. I see nothing wrong with the act of lifting the leg. In fact, I think it's a much cleaner way to pee. The pee gets all over the tree and none on him or his fur.
My boy uses piddle pads too. He typically squats on the pads, or does a squat-and-lift.
My only advice to you is if you want to stop your boy from marking, neuter him once his growth plates close. If he does start to mark before you get him neutered, you can train him not to. It takes a while, but it can be done.