There is an upside. The software has a "run job perimeter" button which will run around the outside edge of your drawing or file. If you do this with the lid open you will be able to see where you need to place your material and the laser wont fire. Since it came with a handy dandy laser pointer, this function can show you exactly where the laser is going to cut.
I decided to take it one step further. I used the laser to mark a line on the bed of the machine (this took burning through a piece of paper to actually work). I then bought a metal square from Lowes (inches of course). It would have been nice to find a metric ruler. I bought an aluminum ruler so I could cut it in the studio with the jewelers saw. The max cut area is 20 x 12 and the square I bought was 18 x 24 so I needed to trim it to even fit into the machine. I cut the square to 20.25" x 12.25" just in case.
Once I found a corner I adjusted the ruler to match the homing program and used the laser pointer to make sure the ruler was perpendicular. Once the ruler was in place I scribed a line with a mechanical pencil, removed the ruler, added double sided tape (the thiner, carpet tape variety), set the ruler back in place, pressed down firmly on the ruler and viola! A square edge for registration! It is not perfect but at least it is close enough to have a reference edge. It also gives me something to push the honeycomb board against for cutting thinner stuff. It is also not permanent so if I need to remove it later I can just pop it off.
The next step is going to be a better table. My studio is literally on the train tracks. The table that the laser is on is from IKEA (total garbage but the perfect size). It could be perfect. Maybe I can still use the top for the new table.