The short answer
Usually in the Dadès gorge or in Ouarzazate. The classic plan sleeps in the Dadès on night one, after crossing the Tizi n'Tichka and stopping at Aït Ben Haddou, then reaches Merzouga the next afternoon through the Todra gorge. On the way back, a night in Ouarzazate breaks the long return.
In more detail
Merzouga is about 560 km from Marrakech, too far for a pleasant single day, so the stop is part of the plan, not a compromise. Our route guide gives the leanest split as Marrakech to the Dadès via Ouarzazate on day one, then the Dadès to Merzouga through the Todra and Erfoud on day two.
Ouarzazate is the other common stop: a larger town with more hotels, close to Aït Ben Haddou and the film studios. Sleeping there on the first night makes day two longer; sleeping there on the last night makes the return to Marrakech easy, with the Atlas crossed in the morning.
Expect kasbah guesthouses and small hotels in the gorges, many with views over the valley. Nights there are cold in winter too. Your Marrakech riad will usually hold your main bags while you are away, so you can travel light. Tell us how you like to travel and we will choose the stops: some guests prefer two short days, others one long one and more time in the gorges.