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.
What software are you using to slice the files? I think that pretty much every slicing software has the ability to add and arrange multiple objects to be sliced together. That is why I like to post separate files instead of build plate groupings so that people can combine the parts in the way that works best for their own printers.
Thanks for the compliment and please post a make when you get it done!