If one motor is slaved to the other, Mach3 will automatically square them when homing.
Make sure that in General Config, "Home Slave with Master" is NOT checked.
If it doesn't appear to be working, you may need to modify the homing script to use RefCombination for the slaved axis. There's info on modifying the homing scripts in the back of my 2010 Screenset manual. http://home.comcast.net/~cncwoodwork...0%20Manual.pdf