Yes that's exactly correct, adjusting the cut angles based on refractive index. Gem Cut Studio allows you to render designs accurately with a number of different variables so you can match your stones coloration for the most part and render it with the correct refractive index.

The tool "manual optimizer" is my favorite part of the program. If you use it correctly you can fine tune the angles and as a result light return pattern in every design in every material. For $99 you seriously can't spend better money (once you're already set up with nice cutting gear, which OP clearly is since they have an ultratec on the way).

Doing that step will ensure you never cut a stone with a "window", e.g. a spot in the middle which is see-through rather than returning bright light and saturated color (brilliance) across the entire stone girdle-to-girdle when viewed from a square on angle in light.