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.
I haven't used Cura, but there's got to be a way. If you can't figure it out, I'd recommend downloading Slic3r PE. You don't need to use it for slicing if you don't want to...but you can import the model, it's very easy to orient correctly, and then re-export the STL file.