Important rituals are usually associated with mountains (and man made mountain/pyramids) and in caves or other accesses to the underworld.
The basic cosmology employed throughout Mesoamerica is based on a three tiered system with the upper world, the world we inhabit and the lower world. The locations of the various ceremonies take place at access points to the upper and lower worlds.
Those folks you saw were likely "cofradias" or day keepers. The are shamans and have extensive networks with others of similar belief. They still wield a great deal of influence in the more traditional areas and membership if considered a status position.
It does not surprise me that you would see them inside the church although, my experience has been more that they make offerings outside.
I think the Catholic church long ago accepted that they would never fully convert the Maya people. They try to include them in their rituals and work slowly at moving folks away from the traditional ways. So far that has not gotten them that far.
Many of the shrined throughout the area have crosses that the casual observer thinks are Christian. Most are not. They represent the world tree (which connects all three worlds). It can take many forms. One of the most common if the maize plant. Many of the crosses you see are painted green to denote their vegetal nature.
To this day there is a heavier presumption of Catholic influence by some that do not speak Maya than really exists. This comes largely from the translation of the work "Santo" which the Spaniards translate as saint. The Maya refer to "santos" a very different entity not having anything to do with catholicism. To them is translated a lot more closely as "spirit".
In the shrine you almost always see Jesus and the virgin. But they are not central figures at all. They are usually small and off to one side. they are just one more in the large set of supernaturals they are concerned with.
Edited to add a cross shrine shot. Maya cross shrines typically have three crosses. ANother dead give away:
![](http://aal.ucsd.edu/reserves/va126bn/210922.jpg)