I don’t see a way to do that, you can include a created mark into a route which makes it a waypoint, but I am not finding a way to take a waypoint that was created using the quick route tool and converting that to a mark that will show up in the “marks” menu under the voyage planning menu. I am curious as to what you are doing that would require that. I didn’t realize that was a thing until you asked.
Also, you cannot use a mark, as the first waypoint in a route using the quick route tool, which has always been a frustration to me. If you click “new” and “quick route”, the first click has to be on a blank area of the chart. Your additional waypoints can be clicked on top of existing marks, but not the first one. Not sure why, perhaps a mod can answer that. There are lots of little caveats in CE that trip me up when I try to use it for more than it was intended. Like building a set of survey lines. CE is tedious trying to set that up, it would be nice to be able to click a few menu items and get, say, 6 parallel lines, exactly 200 yards between centers that were 1 mile long with a continuous U turn at the ends. And why can I not get a continuous turn instead of straight lines navigation only? Enquiring minds want to know LOL.