When using the home switches to square the gantry, the squareness is normally dictated by the switch position. To set up the slaved motor in UCCNC, you go to the master axis setup page, and select the slave from a drop down list. That's all there is too it.
From a usability and setup standpoint, there's very little difference between UCCNC and Mach3. And CNC drive has an active user forum for UCCNC, and excellent support.