electrical guys! i need help bad!

so i swapped from an auto column to a manual column for my 5 spd. swap. i got it in today,plugged up the plugs thinking they are the same,but obviously they are not! i also need to know what wires to use for the neutral start circuit. the plug on the 5 spd. trans has two wires and the factory wiring has three. i hope someone can walk me through this because i don't trust people working on my car. i suck at electrical stuff and i need some help bad! i have too get at least 500 miles on this trans before i go to a race in nashville at the end of may.