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'm using slic3r with no problem at all, I've tested it on Cura with no problem as well. I've never used Simplify3D or ReplicatorG so I can't help with this. If they not intersect the base, slicer may tell that object is not manifold - this is why I did it. This is designed with Blender, I can send you editable files, just PM you email to me. Thanks.