As far as anyone can tell (which isn't very far) those circular pits were used as 'kivas'. They held some sort of semi-religious significance, but what sort is nearly unknown. Some Puebloans use the kiva as a simple sweat-lodge, some use it as a 'sprouting house' for initial crop growth, some use the kiva as a church-like ceremony building, some use it as a giant drum (really). Since most of the Puebloans came to Chaco Canyon in it's heyday and had interactions there, it's very strange that they all then evolved to have different uses for such a special place. The Santa Ana Puebloan People think that there is a sipapu, or 'world navel', just off to the western side of that North-South dividing wall, so there's that as well. An interesting thing is that the Puebloans all met at Chaco, that is fairly well understood, but genetic studies show that they did not interact enough to mate and have children with the other groups. Despite the annual interactions, they remained distinct peoples.

Acoustic studies of the kiva pits show that giant drums, beaten with the feet, had resonances that may have interacted with canyon walls too. But the largest kiva in existence at Chetro Ketl, perfectly south of Pueblo Bonito, is no where near the canyon walls and the size of the kiva makes the resonance in the far sub-sonic for human hearing. In the kiva at Chetro Ketl, there is also evidence of layers of burn sand and dust going down many meters into the ground. There's at least a dozen PhD theses waiting in that dirt.

Also, the layout of Pueblo Bonito is only the first few stories of the building. For preservation, they have buried the lower stories of the pueblo. When you look at the full design plan, it makes zero sense. The mostly rectangular rooms have doors that lead to all kinds of weird places. There are nearly no hearths, and the rooms would have been in total darkness, as little evidence is found of suit on what remains of the roofs (lots of destruction has taken place, so who knows in the end).

We do have evidence from the oldest parts of Pueblo Bonito (the Pueblo was built in stages over about 300 years), that near total darkness was the norm. Skeletons of macaques (yes, from the Yucatan!) show severe deformities associated with lack of sunlight. Also, pottery shards have cacao residue on them from other parts of Central America. The oldest part of Pueblo Bonito is also the only part that has burial of human remains. There, 4 people (likely some form of sub-priest) were interned above 2 other people (likely higher priest-like persons), one of whom likely died of leg wounds just before burial, all in the structure and above the ground level at the time. Coincidentally, half of all the turquoise ever discovered via archeology was found with these 6 people. That's a LOT of turquoise. No other bodies have ever been discovered in the Canyon and very little 'trash' is in the Canyon as well.

Sorry for the ramble. But Chaco really is a place of questions, not answers. It's very unique in the world for this reason and well worth the visit and deep-dives into it.