I keep a binder and note book in the trunk that has all of my modifications in detail along with part numbers so if I ever sale the car or forget what I need to replace a part I have a quick reference.
Just tape the tips of the wires that aren't needed and zip tie them to the rest of the harness. What I did in my old ES when I installed the carputer I used a cheapo harness adapter and just followed the color code. Red to red, yellow to yellow and so on. It sounds like he's hard wiring the deck harness to the car's stereo harness. I would use the diagram from the12volt.com and label the wires or write up a reference chart for what wire does what.
Deckside or harness Adapter
Most stereo configurations use this format for color coding.
1984 - UP dodge stereo harness.
Gray Connection Block
1 Pink/Black = Memory
2 Red/White = 12volt power
3 Orange = Dimmer
4 Black/Yellow = Illumination
5 Blue/Red = Right Front -
6 Brown/Red = Left Front -
7 Not Connected
Black connection Block
1 Blue/Orange = Right Rear -
2 Brown/Light Blue = Left Rear -
3 Violet = Right Front +
4 Green/White = Left Front +
5 Blue/White = Right Rear +
6 Brown/Yellow = Left Rear +
7 Light Green = Amp Trigger