So on the stock system, this is under the passenger seat. Would this just be the amplifier module, or something else? Ie can I safely ditch this to put my aftermarket amp under the seat? Would be a more convenient location than the boot...
That is the AUD module. It's not just an amplifier, it does the digital to analogue conversion as well. The connectors from right to left are:
2) Primary MOST bus (optic fibre)
3) Speaker outputs
4) Secondary MOST bus (unused)
You can't remove it as the IAM only outputs a digital stream which the AUD then converts to an analogue signal and amplifies. The traffic on the MOST bus is packet-based (like ethernet) and as well as sending the packetised audio the IAM also controls the AUD output via control packets over the MOST datalink (i.e. the volume, balance etc).
If you want to fit a sub, you are going to have to tap in to one of the outputs in the third connector and do high-to-low level conversion to a separate amp (or have a sub amp that accepts high-level inputs).
It's a 16-way connector and the pins for the speaker connections are assigned as follows:
(Grey/Black) & 9
(Green/Black) - Left Front
(Grey) & 10
(Green) - Centre Front
(Yellow/Black) & 11
(Violet/Black) - Right Front
(Grey/Red) & 12
(Green/Red) - Left Rear
(Yellow/Red) & 13
(Violet/Red) - Right Rear
I would tap in to one of the front or the centre speaker connections, as if you have got dolby surround enabled I think it applies some delay processing to the rear channels.