You assign one extruder to one stl and the other extruder to the second extruder would be the normal procedure. If you have one of the dual color prints you normally need to put both into the same group. Drag the object on the rights sidebar on the other one to group them so the 2 together build the complete model.
Make sure host and slicer config are set up to use 2 extruders as well!
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Make sure host and slicer config are set up to use 2 extruders as well!