I'm just setting up my mach3 interface so I could be way off on this, but....
I just configured my e-stop and limit switches. The switches on mine are all normally closed except z home which uses the touch plate.
All my switches are connected to the breakout board through the DB9 connection that tie to the breakout board. E-Stop is pin 1 and 9 on the DB9 I have all the limits and homes (except z-) wired in series and tied to pin 8 and 9 on the DB9. z- is hooked to pin 7 and 9 on the DB9.
Hope this helps some.
If you need the wiring from the DB9 to the breakout board let me know, I'll trace them out.