OK, so I think I've made some progress on this - I hope this will be a useful post for others who are trying to do something like this!
I found a fuse guide for an E320CDI 2004 which seems to have a similar layout i.e. Fuse 14 is not used in the diagram it seems - and nor is there a fuse in mine.
I understand only the estate has a trunk/boot plug socket (I can't find one in mine) - and the rear one I guess is under the centre console for rear passengers.
I am going to ground to the chassis as I read someone this is worth doing to avoid situations relating to a flat battery.
Is there any reason why I can't take the power for the active subwoofer (15A rated fuse inline with the power on it) and take the switched remote control from Fuse 12 (or even just the power from Fuse 12 and the remote from Fuse 14 if not)?
I can then use the high level input and take the input from the stock sub, which would remain disabled and probably has low pass filtering already.