Some times the PCB manufacture sends PCB panels with bad circuits, there are three ways to make these PCB without placing parts on the bad circuit, Well two in fact plus my method.
(1) Placing a light mark on a dark background (or reverse) then the camera will check each circuit in turn, then put parts on the good circuits. NOTE: This was the first method I was taught, and in a way would prefer this method.
(2) changing settings from "matrix PCB" to "non matrix PCB" and deleting the circuit X, Y, degree, settings on circuit you dont want. NOTE: This method is not too bad, however, the person who showed me (from another company has gone) and every time I use this method I loose the "First circuit", "Number of boards" & "Pitch between circuit" settings. I am sure when the other person showed me he never lost these settings. But good for doing sample boards and you dont want to screw up multiple circuits, when there is a engineering error, you do one when that works or if errors need to be fixed you make all the rest of the circuits.
(3) At one stage one of the machines would not work on method (1) and at that stage I did not know about method (2) so I tried my own solution, this works best when you have a matrix of 2 by 1 you change "Number of boards" from 2 by 1 to 1 by 1, to do the left circuit you just put the boards through the machine, To do only the right circuit you have to change the "First circuit" setting if it was -4 and the width is say 94 you change the setting to 90 and it will only place parts on the right circuit, (sometimes the machines complains, but ignore error message, just make sure your mathematics is correct.) This is a brilliant method for doing 2 by 1 circuits, it can be set & taken off in seconds, you can do 2 by 2 but you have to put the boards in twice changing the settings each time before hand, bit of a messy way of doing it, only try it if you are desperate, as we were once when we had a load of rejects.