In my bedroom, I have a DirecTIVO machine but it doesnt support HD (this is where the signal goes first) then from that machine I have it wired to a DVD burner (so I can record something off the TIVO if I want) then from that burner to the TV. If I buy a HD tuner where would it go in the string for it to work for over the air HD signals?

Hook the HD Tuner to a separate input on the TV. You won't be able to record the HD broadcasts on the DirecTivo.