I gather that each of your data sets is a big collection of geo data, like arrays of coordinates?
Putting an entire data set into a single document isn't the way one would normally do it. Any database works best when you keep the documents/records/rows small, because generally these are the units of I/O. Also, in Couchbase Lite documents are the units of replication, so any change to a document causes that entire document to be replicated again.
As for querying, databases generally aren't good at queries within a single document/record; instead they search across records. In Couchbase Lite it is possible, with some creative use of map/reduce, to index and query within a single document; however, I don't recommend this because it's not future-proof: version 2.0 is replacing map/reduce with a more traditional query language based on N1QL, which is a lot more powerful in most ways but doesn't support some of the use cases of map/reduce such as this one.
What I'm saying is that it would be best to store each "item" in a data set (whatever the granularity of an "item" is for your use case) as a document. You can still store multiple data sets in a database by tagging the documents with some property like "dataset" whose value is a unique identifier.