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 not sure about Simplify3D but I've heard that Cura can do this. My concern is that sometimes PVA-over-PLA isn't a strong bond (which I think is a reason that the prime tower falls over), so the support interface might not stick well enough to the supports and you could have a fail at that point? I'll let you know when I try it...