Hey Pat,
to square a machine with limit sensors when you have two Y drivers (Y and B software-slaved on the Masso) and therefore two Y limit sensors, you can adjust the rectangularity (“squaring”) by moving one sensor back or forth by the amount that your machine is out of square (see also here). However, I think it’s good on assembly of the machine to make the machine as square as possible. See here for checking and adjusting rectangularity (“squaring”).