I visited this WHS in September 2016 during my Latin Grand Tour which last for 7 months. This is a very interesting WHS as most of the WHS in Latin America are related to Aztec, Mayan, Inca or Spaniards glory history, and Joya de Ceren is more to the daily life of the Pre-Columbian Mayan 1400 years ago. The ashes from the nearby Loma Caldera volcano eruption covered and preserved the site in time capsule, just like Leon Viejo and Pompeii.  

I recommend to visit the museum first before entering the archaeological site so that one will have a better understanding of what's in the archaeological zone. Most of the excavated items are here, for example you can see many ceramics with drawing of animal found in jungle like monkeys and birds. The most interesting item I found in the museum is the carbonized corn. This is the evidence of Mayan domestication of plants and up till today the Latinos are still eating corn as their main food.  

Joya de Ceren was a small Mayan village with 10 structures including some houses and storehouses. There is also a temazcal where the Mayan used as a sweat lodge to heal sickness. The site is not big and it will only take you around half an hour but interesting enough to be the only WHS in El Salvador.