My amp is mounted in the boot as there's less distance for power (Cooper S). I then ran the RCA cables back from the head unit and ran the speaker cables back to an ISO connector to the original harness (saves running new cables to the doors.
Upgrading the speakers is very worthwhile though I only did the fronts - albeit with some high end JL Audio ones.
Now: 2005 R52 MCS
Plus: BMW X3 3.0d, BMW Z3 2.8, BMW F700GS, Vespa ET4 125
Was: 04 R52 MCS, 06 R53 MCS