Things I learned about the HK system
Head Unit (HU)
You can replace the HU with an aftermarket unit but please buy the electronics that will allow you to control the HK amp and utilize it's EQ settings.
The original HU really doesn't work as you might think without the HK amp hooked up.
It has no preamp outputs. (you can add them by taking the unit apart and soldering RCA leads off of the preamp output section) (From what I understand though this is not recommended - produces distortion) (if inclined see great other posts)
The sound level (loudness) is controlled back at the HK amp. (without the HK amp you have no volume control)
There is no "rear" speaker output to the HK amp. That output is generated in the HK amp and is a fixed balance of the front volume level. Depending upon the "fade" control.
The "fade" control in the HU is a fake out. All that really happens is that "fading" to the rear decreases the front volume.
Working in the front seat area is relatively easy, but be careful when disassembling the upright side columns. They can scratch the dash.
Cover all areas with towels or the like to prevent the scratching. You'll be glad you did this.
Read all helpful disassembly advice before you go down this road.
The area behind the HU appears to have alot more room than was indicated in the discussions I read.
Harmon Kardon Amp (HK)
The output of the amp is not common ground. They are normal (+)(-) leads. (I did read this about many BMW installs)
There is only one set (left/right) inputs to the HK amp. These are from the HU. Front L/R into the HK amp.
There are eight HK amp outputs. Four distinct sets of (right/left) outputs going to three speaker groupings in the car's interior.
Door full range (5.25 in)(6 in)
Tweeter Combo in Door (midrange and a smaller tweeter coupled by a capacitor)
Rear dual coil (6x9)(one speaker handles two separate outputs from the HK amp) Note DUAL COIL (TWO INPUTS) (ONE SPEAKER)
The wiring diagrams I reviewed online were not totally correct.
They were extremely helpful and a wonderful starting point but colors, functions, and/or no connections needed some adjustment.
The HK Amp plug shell comes apart easily.
Cut only the wires necessary.
There is plenty of room in the boot side panels for hiding wiring / crossovers and other stuff you add-on.
Wiring diagrams are here: