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.
There is a zip file that contains images of all each file in the correct orientation.
I'm using Slic3R PE, and most files come in flipped sideways, IDK about your software.
For the most part, it's pretty clear which side should be down for the best results - so if the file doesn't look right when you import it, just change it. I mainly just flip it to what I think is right...but then if I'm not sure, I'll check the zip images he has.