You can start with the top panel or the bottom. It doesn't make much difference.

1. Open xcs, and open the first file.
2. Set the file to the center of your workspace.
3. Click the layer and set your settings for whatever material you will be cutting from.
4. Place your material in the laser and Focus.
5. Once you have focus, close your lid (as much as you can) and pew pew that start button.
   
   Once completed, repeat the above steps for the second file.

Once completed, you should have two pieces that look like this.

Be careful with the top piece as it's a little delicate until it's affixed to the bottom panel.

1. Using extra time GEL super glue, apply a thin line on the top, bottom and center of the top panel. Be sure not to glue too close to the oval holes in case you use the screws to help align.
2. Pace the top panel on top of the bottom one and ensure that they are aligned. 

I ended up putting them together and putting the screws into the holes at the top and lightly securing it to the baseplate of the laser. I then pressed down and left on both panels and checked the bottom to ensure a proper alignment. I then tightened the screws and placed a book on the bottom half to apply pressure.

Now that you have the jig made, create a file in XCS that is the size of your business card. 

Before you secure your jig down, place a card in one of the side panels and focus your laser.

insert the screws into the top of the jig and center it on your workspace.

align a left and right business card shapes in XCS to the shape of the cutouts (I found that it's easier to do one, then the other. there is about a 5mm gap between the two).

Once you have everything aligned, tighten the screws.

Place your business card art within the confines of the boxes on your XCS and either turn the boxes to “ignore” or remove them (I find that ignore is better so you can save the file for future use).