I can't give you a definate answer for the 3.0 TDI but i'm guessing it may be similar to the 2.0 TDi possibly.... I fitted a tunit box to my girlfriends old A3 2.0 TDI which was a circular rotating plug on the cylinder head (to the gearbox side). Also fitted a similar box to my old Range Rover TD6 and that was found in a similar place.
When you get the box it'll be fitted with a plug that will/should only fit in one particular location. Its usually a case of unplugging the original loom, plugging the tuning box into the engine side then refitting the original loom into the other end of the tuning box wiring. They always fit them in line from past experiences with different cars (I've fitted about 6 or 7 in the past 5 yrs or so).
All that said I might be way off the mark, it may be an idea to have a look on a few diesel tuning companies websites just to check for alternate instructions. Tunit wanted £50 to print out some instructions for my range rover box which I bought second hand off ebay, I told them where to go and managed to get info off a fellow forum member.
I'm sure someone with a 3.0 TDI fitted with a box should be able to shed a little more light onto its location
