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 don't use Slic3r, but you have to use the support setting equivalent of 'from build plate only'. You do not want supports inside the cooling channels. If Slic3r does not have such a setting, then use the free Cura slicer.