If you use a 12"x12"x board you won't have to do any exterior cutting.

I place my honeycomb in the upper right corner of the S1 bed and then place the 12x12 wood at the 4" mark flush at the bottom. 

Make sure your cutouts are where you like, adjust if you need to and process with the settings attached for the S1 10w.

You can then later ignore the cut and engrave layers and use the template to keep add your desired engrave designs and keep them in the same spots as you batch out product!