As of right now, MapReduce jobs on a single mongod process are single threaded. This is due to a design limitation in current JavaScript engines. We are looking into alternatives to solve this issue, but for now if you want to parallelize your MapReduce jobs, you will need to either use sharding or do the aggregation client-side in your code.
Even when a permanent collection name is specified, a temporary collection name will be used during processing. At map/reduce completion, the temporary collection will be renamed to the permanent name atomically. Thus, one can perform a map/reduce job periodically with the same target collection name without worrying about a temporary state of incomplete data. This is very useful when generating statistical output collections on a regular basis.