The functions available on the HU are limited to adjusting subwoofer output and recalling memories in the PXA (such as levels, time alignment, etc) to make any adjustments, you have to access the PXA controller. I wired mine into/through the rear console, so it's somewhat accessible-it'll reach all the way to the front seats, so when I'm done making adjustments I coil it up & stow it in the rear console.

As to time-alignment, the device aligns all speakers it controls to a single location-in my case I aligned to my head (you suspend a small microphone where you want the reference point to be).

It'll work with with either configuration you describe.

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"If God had meant for us to walk, why did he give us feet that fit car pedals?" Sir Sterling Moss

Michael
2014 E63S Estate
2006 SLK55
1995 E500
1986 Porsche 944 turbo