Its easy to run new cables everything goes down the centre tunnel or under the left hand and right hand lower front cowling, same as the oem wiring, easy enough to do, just one thing to remember is when putting in an amp make sure it has short earth lead otherwise you will get ground feedback.
There are a number of options for the sub, but having it play upwards from the hoops is no good when the roof is down. There were two subs fitted to the z3, one being the HK which you can take out the old speaker and with a little mod fit a Kicker CVT into it. I based my sub but did not want to spend 80 - 100 quid on the kicker sub, so went the hi fi root on this and made the sub enclosure out of 12mm MDF, works fine but will get a better fit using 6mm (version2) this enclosure sits where the original sub sat and plays forward into the cabin, providing the fill and base that is missing, and looks OEM only sounds better