What we have seen of the Glowforge interface so far, it is even more user friendly than most lasers. So the answer for this product is likely nicer than the answer I can give.
But, to answer for how lasers I have seen so far behave:
You set up your file for printing with whatever color scheme you desire. Just make sure that if any two lines or fills share the exact same RGB code color, you want them both cut with the same speed and power.
Once you are ready to cut, you load the file to your laser software, and you tell it which colors to work with at all, and what speed and power to use for each color.
There is no magic “You must use this precise shade of red, and that shall always mean a cut straight through!”
Those kind of rules are put on you if having someone ELSE run their own laser cutter for you. This prevents them from having to ask every customer every time “Are you SURE you wanted me to cut the green? Which shade of green was cut, and which was engrave? Did you realize you used 27 different shades of blue?..”
But… you may wish to impose such rules on yourself, so that when you open a file from years before, you can remember what to cut and what to engrave.
The signs of the glowforge being even better than this… we have seen someone use a pure black image, and engrave one section, while cutting another. The software identified the circle outline as a different segment from the solid fill pattern inside of (and not touching) the circle.
So, this is a level above and beyond what I have seen on any other cutter interface. And even more so provides the idea that whatever you design now… it will work how you think it should work (95% of whatever you do at least)