One of the greatest Mayan ruins sites on the peninsula, Calakmul is also a jungle paradise where you can see many local animals; including - if you are very lucky - the elusive jaguar. If you are looking for a "lost city in the jungle" this is definitely it.
The trip I recently did was Merida - Campeche - Champoton (lunch by the sea) - Escarcega - Xpujil where we overnighted in a small but decent enough hotel. The next day was spent at Calakmul and we returned to Xpujil for the evening. On the third day, onwards to Chetumal where I left my guests to take their flight back to San Miguel de Allende via Mexico City. The drive back from Chetumal to Merida takes about 5 hours if not making any stops.
For a future trip I would spend more time in the area, as there are many other ruins sites to visit. Perhaps 5 days total leaving from and returning to Merida, making stops here and there during the driving portions of the trip.