There are now a couple of ways under development…the most recent addition is still in Beta…it’s called Snapmarks, and they are the precursor to the alignment software that the Glowforge team is currently developing. (They allow for perfect alignment…very nice, but they are not available to everyone yet, they are being rolled out to various machines for testing right now.)
So if you do not have the little magnet icon for Snapmarks displayed on your app yet, you can still use the jig method to use the Passthrough with good alignment. We have a couple of tutorials that lay out the method here: