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.
How it is wired up depends on your hardware and firmware. Here is a writeup for the lulzbot TAZ (which uses a RAMBO board). You can see a writeup of how it is wired here: https://forum.lulzbot.com/viewtopic.php?f=36&t=4923. I also connected it up for a Kossel printer running stock Marlin firmware and RAMPS 1.4. There is used the default pin (pin 4 which is on the Servo 3 header). You have to enable the function in configuration.h.
When the function is enabled, it will lift and move the head away from the print and the pause when a filament runout is detected. It makes a clicking sound to alert you that the filament has run out. Once you change it, you proceed with the print by pressing the control knob on the LCD panel. It then returns to its original place and resumes printing.