Hi Alireza,
Right now there is only one option, the IndexProvider implementation, which allows you to view the spatial index as an index in cypher, and access it using the 'START n=node:A(B)' syntax, where 'A' is your index name and 'B' contains your query. This only allows a limited set of possible queries.
Our own plans to add spatial functionality to Cypher will be quite different, based more on the newer 'Schema Index' approach in 2.x, and allowing spatial functions in the cypher predicates themselves (in the WHERE clauses). This should be more intuitive, but ill not be available for some time. This support will be part of an official neo4j release and as such have documentation included in the normal neo4j documentation.
The documentation for the older spatial library is a bit scattered unfortunately. And I think Jim's answer looked like a particularly comprehensive answer to me.
Regards, Craig