I found a post on another thread here that explicitly says you can define which colors map to which operations:
Continuing the discussion from Watch Brad Feld & Dan Shapiro print something:
In the video in that thread, it appears that the Glowforge software auto-selected cut for the vector circle and engrave for the raster image inside it, but I am guessing based on @dans comment that if you wanted to vector engrave some stuff, you would just need to make those lines a different color than the cut lines and then tweak the settings on the left side before you hit go.