Lack of documentation seems to be a problem with S3D, the stuff they have on the site is good, just not even close to being enough..
This will explain the separate process.. and I saw a post or article someplace that explained how to add some gcode to the the end process script that would move the bed for filament change and the some to add to the start of the next process to put things back where they need to be..
https://www.simplify3d.com/support/tuto ... f-a-model/