If we want to look at it as a phrasal verb, then "punch (something) in" means to punch something so hard that it collapses inwards. It's the same idea as "kick the door in". I agree with Spagnola - please don't use the other phrases, including "punch you on your face" and "punch on your face". None of them sound natural - they actually sound cute and funny - and you'll just come across as someone who really doesn't understand English at all. For the phrase "punch your face in", you can use kick, beat or bash instead of punch, and head instead of face.

The typical placement of "in" if after "you". " I will punch you in the face."

Lol no they don't all sound fine. Especially "I will punch your butt in" - please, never say this. "Punch your face in" - is just a phrase native speakers use to threaten someone. It means you're going to punch someone until their face caves in.