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.

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Try this fw:
http://www.marlinkimbra.it/. Using the online configurator and setting 2 as the number of extruders you will ha ve the choice for "Dondolo".
With this fw you surely have the possibility of stting the Z offset for both.