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.
One little thing to watch out for, is that once rotated, be sure the model is sitting flat on virtual build surface (not floating or sunk below zero Z level). I'm not familiar with how Cura works in that regard. Simplify3D has a "drop" function. This lets you spin things around, then pick them up and drop them down to the build surface.