Taken straight from my NOS 5116 Nitrous kit instructions:
One wire of the harness to each coil will have the same color from coil to coil. This is the ignition start/run wire. DO NOT USE THIS WIRE. Use the other wire, which is the negative lead. The negative wire is the smaller gauge wire and color-coded differently for each coil to differentiate their cylinder location and the firing order of the engine. Any cylinder coil may be used, depending on the desired mounting location of the window switch.
I ended up using the 2nd from the front of the car on the drivers side for mine.