MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
In short you can only have one gear per part file. There are several different ways of extracting a dumb model and inserting several non-configurable gear blanks into a part file and create configurations that way. Check with the solidworks community for tips on how to do that.