If you're using the aftermarket wiring harness to go between the new deck and the SHO harness, the SHO wiring shouldn't matter. Most good adapters have each wire labeled right on the insulation of each wire. It should just be a matter of matching each wire in the aftermarket harness to the wires from the new deck (there should be a diagram for the deck wiring in the manual). As for the amp in the car... did your harness come with a harness to bypass the amp? If so, use it. If you run the amplified signal from the deck into the amplifier in the car you have a good change of frying the deck, the amp, the speakers, or any combination of the above. I got my harness from Best Buy when I bought my deck and it came with a bypass harness for the amp.
If you still need to know wiring colors...
Most Pioneer decks -
P o w e r
Memory (+12v Constant) Orange
Ignition (+12v Switched) Red
Ground (-) Black
Illumination Yellow
Phone Mute Yellow/Black
Power Antenna Blue
S p e a k e r s
Right Front (+) Gray
Right Front (-) Gray/Black
Left Front (+) Green
Left Front (-) Green/Black
Right Rear (+) Gray/Red
Right Rear (-) Black/Gray
Left Rear (+) Green/Red
Left Rear (-) Black/Green
Most other aftermarket decks -
P o w e r
Memory (+12v Constant) Yellow
Ignition (+12v Switched) Red
Ground (-) Black
Dimmer Pink/White (Alpine only)
Power Antenna Blue
Amplifier Turn-on Blue/White
Phone Mute Light Blue (Sony only)
S p e a k e r s
Right Front (+) Gray
Right Front (-) Gray/Black
Left Front (+) White
Left Front (-) White/Black
Right Rear (+) Violet
Right Rear (-) Violet/Black
Left Rear (+) Green
Left Rear (-) Green/Black
Hope this helps!