Should I go to Merzouga from Marrakech or from Fes?

Via Marrakech for the kasbahs-and-gorges road, via Fes for the shorter drive and the Ziz Valley — ideally arrive from one and leave toward the other.

The through-route is the smart itinerary: no repeated roads and both imperial cities in one trip. If you must choose a single base, Marrakech offers the more spectacular (if longer) approach.