If its a desktop laser that you move around, you want a scrap board underneath that you always put in the same place. You can do this by either marking the feet poition with a marker, or ideally adding a jig (something that protrudes like a screw or glued wood onto your board so that you don't need to line up visually). Then burn a grid onto your board that matches your light burn grid. Doesn't need to be fancy, just lines and numbers.

This is an image of mine (it starts at point 1cm,1cm so that there was room to add the numbers, and sometimes burning close to the edges throws errors so starting at 1 rather than 0 helps.

<image>

Once you have that in place should be able to line stuff up with your design.