Your slave axis will not move independently unless something is wrong. You adjust your switch in or out on which ever side you want. That will eventually square the gantry to the table. The gantry backs off the switch a specified amount each time it homes to it. The clears the switch. Adjusting the switch in or out changes where that back off stops. It will do it for either side, but best to just choose one side to manipulate. Since your machine is square, it should work correctly that way.
You will need a known good square to check with. At least that is what I use. Then I actually make cuts 90 degrees to each other in scrap and check those out.