You are correct, the PTC's are in front of the shuttlebay. Main engineering is directly behind the shuttlebay, with the reactor itself being turned on it's side 90 degrees so that the matter and anti-matter comes in via the side, and the PTC's exit from the bottom and top.
I'm a bit shocked, though, as I'm sure I made a start with Main Engineering but I can't find it anywhere anymore
[EDIT] Ah, here it is! As you can see, the back of main engineering and of the shuttlebay are back to back. I'm looking at the possibility of adding a wall in between htem, as this would protect main engineering from a crashing shuttle