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.

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If I'm not wrong, your slicer needs two files to print a dual model, thus yes, you need to download two different STL's, one is not enough.
You may like to take a look in the "Instructions" tab in order to know which two files you need for a given model.