So, here's what I'm doing: I have a flattish box; 80 x 50 x 5. I have letters that are 2mm tall on one face and letters 2mm tall on the opposite face. I've done them as two STL files:

1. STL model with the words. One set of words is on the platform, 2mm tall. Other set of words is 2mm tall and raised 3mm from the platform.
2. STL model of the box itself, just the dimensions listed above.

In Simplify3D it centers the two together, and I've got separate processes printing each model from a different extruder. White for the words, red for the box.

However, it's putting down the first layer as all red -- then starting the white letters in the second layer.

Is it necessary to make a hole in the box which aligns with the letters? Or is there a way to override in Simplify 3D and say, "Where these are flush, one process/extruder has priority?"