The Secret Caverns are where Ruby and Chomper stay at night when they sleep. It is seen briefly in various episodes, although a lot of them are seen in the TV series episode "The Cave of Many Voices", suggesting the caverns to be quite extensive.
In the time before "The Cave of Many Voices" where Chomper and Ruby have to find a new cave to stay in they seem to be sleeping in the first cave or so. During this episode Chomper finds a new cave for them to stay in.
Some places seen in "The Cave of Many Voices", but not seen in any other episodes are things such as an underground water fall, and a Cave of Many Voices that the episode is named after. With the glimpse we see of some of the areas farther in of the Secret Caverns in the episode The Cave of Many Voices it would seem they are quite extensive.
Since Chomper seems to know his way around in the episode it would seem to indicate that he has done some exploring and knows at least some areas.
The Secret Caverns joins the Cave of Many Voices in the first Land Before Time episode on air called "The Cave of Many Voices" where Ruby and Chomper stay at night when they had to sleep which they are quite extensive. Some places were seen within the cave, but not seen in any other episode like an underground water fall and a Cave of Many Voices was here since Chomper knows some of the places here.