Scrappers organize in many ways. Usually it is what makes sense to each person. On the other hand, I've learned a lot from the suggestions listed in the GDS forums.
So, that said.... I do the same as you (separate GDS folder with each designer's folder inside that.)
When a designer retires I just add _retired to the designer's folder name. For example: Carena's Designs_retired.
Hope this helps. Really, anything that works for you is best.