setting machine to go home on a gantry style router

i wired in my home switches and when i trip them by hand, my diagnostic led light comes on in mach3. i wired 3 seperate inputs for the switches. one for z, one for y, and x.

but i can't get the machine and mach3 set to a permanent home with the switches. i've tried everything.
also,when in diag tab on main screen, and i hit the ref x button, only my x moves, not the a-axis. *note* a-axis is slaved with x asis (gantry cnc router). it jogs fine in sync, but i can't get the home switches set. hellllp!
i've followed the videos on art soft page, followed every tutorial possible.