Unless I've missed something in my reading, colors can't be used permanently.
You can make your colors in RM permanent or not. It's your choice. But there are some caveats.
The first caveat that jumps out to new RM users usually is that color coding is not "dynamic'. For example, if you color code all descendants of John Doe as red and then add a new descendant of John Doe, the new descendant is not automatically red. RM does not store the rules used for color coding individuals as red. Once an individual is red, he or she is red and that's it. There is no indication as to what rule or process or data was used to color code the individual as red. So if permanent color coding is important to you in RM, then regularly you will need to reapply your color coding rules.
Another caveat is that there can be conflicts in color coding and conflicts are not identified for you automatically. If you color code descendants of John Doe as red and descendants of William Smith as blue, and if you have a descendant of both then the descendant of both will have whichever color you last used for color coding the individual.
One of our frequent contributors to these forums has a user defined fact for each person in her database that describes the color for that person. The user defined fact can be used at any time as the criterion for reapplying each color, one color at a time. The difficulty for a TMG user converting to RM with user defined facts is that user defined facts have to be added manually one person at a time. They are not already there as are the flags in TMG.
Until and unless RM solves this problem, my personal advice is to use RM's Named Group facility where you might have used color coding in TMG. Just like RM's color coding, RM's Named Groups are not "dynamic". If you make a Named Group of John Doe's descendants and then add a new descendant, the new descendant is not automatically added to the group. RM users have been waiting since RM4 for a solution to this problem. An advantage to Named Groups as compared to color coding is that there are no conflicts because an individual can be in more than one group at the same time. Another advantage of Named Groups is that you can use them to implement several different coloring schemes as your needs change because it is extremely easy to color code individuals based in their membership in Named Groups. Which is to say, you are probably better off thinking of Named Groups as a somewhat permanent way of grouping your individuals and thinking of color coding as a more temporary way of grouping your individuals.
But as I said at the beginning,you can certainly choose to use colors in a very permanent way. You just have to remember that RM does not constantly re-apply your color coding rules as you add new people to your database.