ZASto is quite right - that is the way to do it. I was using Mach3 with my CSMIO for so long that I had forgotten about this. However, it does need the A and Y home switches to be separate and taken to different input pins on the BOB, and then you need to configure these in "Ports and Pins." Apologies if you have already done this, but it's easily overlooked.

This capability is one of the nice things about Mach3 - you can home multiple axes at the same time. I used to home Z, then Y and X+A simultaneously. Saves time on a big machine to do X and Y at the same time. As mentioned, though, it only works if each home switch goes to a separate input pin, which can be a problem with the old parallel port BOBs (not enough pins).

This thread might help as well. Not the first time that the subject has come up!