That’s the origin I meant indeed 
You’ve set it at the bottom corner of your workpiece. Did you also set as the origin on the SM when you started the job? If you configured the work origin on top when you loaded the job on the SM, then you’ll see indeed that it’s cutting above the workpiece in the air.
As it’s tricky to set the work origin at a bottom corner (you can’t do it in one pass as your drill can go through the material like a ghost, it’s usually easier to set it on the top surface.
Based on the screenshot you posted, I think you should also look into how deep your cut will be. Can’t see real measurements on the screenshot, but it looks like you might be using too big of a stepdown.
This thread contains a lot of useful info on cnc (and laser) to help you get started. Some info on cnc tool changes and combo cnc/laser projects