Of the 20 inputs, which two are for the two coils?

It depends on which pins were used inside your ECU. There's no way to tell for sure without removing the enclosure; so do that, take a few pictures, and post them here.

Originally posted by VelocitaPaola
It depends on which pins were used inside your ECU. There's no way to tell for sure without removing the enclosure; so do that, take a few pictures, and post them here.

What is the "enclosure"? Sorry I don't know lol

its pin 3 and 11 in my ECU.

It can't be pin 11; pin 11 is tied to ground. And pin 3 is tied to ground in the relay board, so you would have to either move it or ditch the relay board.

http://www.bgsoflex.com/mspower/mspower.html

im sorry i was talking about my stock ecu. i am running stock ecu, with megasquirt currently running my fuel. i want to wire in the spark control, and the ignitor is already wired up to the coil, the ground is wired, but idk where the last two go.

are you familiar with the 4g63 ignitor set up?

http://www.2gnt.com/index.php?d=MSnS_INSTALL_(parts/wiring_only!)
http://forums.2gnt.com/dcboard.php?az=show_topic&forum=54&topic_id=776&mesg_id=776&page=

so do i just skip the relay board? lol

Originally posted by bnisson
so do i just skip the relay board? lol

Probably. As you're discovering, it just adds an unneeded layer of complication. Your car already has pretty much all of the required fuses and relays anyway.