Great questions! 
The Glowforge interface gives you the option to Engrave (the etching), or Score (cut partway through) or Cut, if you have used different colors to create the design. It also treats Fills as engraves, and Strokes as either Cuts or Scores. (You tell it which.)
If you set each operation up as a different color (Red for Cutting, Blue for Engraving, Green for Scores, etc.) you can do all three operations at the same time so multiple passes aren’t necessary.
And if you set everything up in your file (SVG format) before bringing it into the Glowforge interface for processing, you don’t need to worry about registration, it aligns design elements perfectly in relation to each other.
If any of that was confusing, a group of Regulars have put together some tutorials that folks can read to learn about how to use the machine before they get it…the one to start with is linked below, and there are a LOT of helpful tutorials on learning to use Design software if you want to get started on a program ahead of time.
Here’s the link to the Design Matrix that cross references all of the Tutorials.