Ok, lets see,
If I was going to wire this type of coil up through the realay, it would be the fuel pump relay just to recieve 12v keyed ignition. Then the others would be chassis ground, megasquirt ground (low reference) and ignition command (wire megasquirt uses to fire the coil) Im assuming you are using full sequential ignition and the goils are gm based with internal ignitors. If im wrong though, please let me know, I just briefly researched this. I personally plan on using 3 bips for wasted spark because im cheap but ill eventually go this route myself. Good luck.