Well the way I was taught to do it was to lock the travel on the Y movement and then hold a pencil at one point on the rule and slide across the X movement. Once you have done this adjust the screws on the rule so the X rule is parallel to the drawn line, then flip the head around 90 degrees and align the Y rule to the same line.

Assuming the head is actually square that is it, however you can check it all works by tipping the head around at 45 and -45 degrees and drawing a line with the X and Y rule, they should be parallel, if not you have to get it as good as you can.
 

One thing I would add to Ajack1's method, is first set your pencil at the inboard end of the x axis and draw a line across the bottom of the board without moving the pencil on the rule.
 Then measure up at each end to see if the machine is set square on the board. Adjust the two clamp screws if it is not to parallel the line to the board. Then go on as described by ajack1.
B.E.
P.S The drafting table I mentioned in the earlier thread I never did get rid of. It now sits on my back porch under a cover, and occasionally I will go out and use it to lay out something, then bring that back in and draw it up in CAD.
B.E.