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.
You should be fine for using a pololu driver on the MK6, you would need to make a new machine profile or run the pololu at 1/8th step. I've run the MK6 motor on a gen 3 driver board, Rob's PSMD (pololu boards), and the Gen 4 driver board. ( I didn't extrude plastic on all the different versions, just run the stepper.)