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.
Also took me a while to realize it.
BTW: I purchased endstops to install a Z-Max on both motors. Then I found they weren't necessary either. To sync the Z motors I just disable software endstops and then run both motors 2 mm lower than they can go. It might not be elegant but it's easy and works.