the two plugs from the stock coil go into the msd harness, and then then the other side of the MSD harness plugs into the coil. I think only the front plug socket is used, not both like in stock config. Then your red/white/black/orange all plug into the msd harness as well. I dont have it in front of me, btu thats how i remember it.
Didnt it come with directions? Make sure you put a fuse inline with the battery.