When you select Load Modifier, it expects an STL file. Any part of the object that this file overlaps can be assigned special settings that are different from the ones assigned to the file as a whole. The Modifier part does not have to match the main file exactly and can, for example, be a cylinder that covers the main part at a certain level. Included in those settings is the extruder assignment, allowing you to switch colors for any part of the object. Other settings include number of perimeters, infill density, etc, etc. Besides assigning colors, you could, for instance, stiffen up a weak area of the design by increasing the infill. Unfortunately Slic3r cannot assign extruder percentages for mixing colors, and the 301 does not allow external control of the percentages anyway, .at least not until we get our hands on the source code.
The parts cannot be moved in this dialog, so the geometry has to be created beforehand in a number of ways. It can be as simple as elevating a small part in Repetier, maybe one made from cutting up the main part in Slic3r. Any CAD program that retains z axis transformations could be used, probably whatever program was used to create the main part in the first place.
When you export the file as .amf, the modifier information is retained. It looks like the gcode works in Repetier-host and Octoprint and probably most other print controllers.
Hope this saves someone else the many hours I spent searching for a solution.
Happy New Year!
--Dave