I want to be able to order which folds go under and which go over is there a function for this?

Sure, you can do this by either providing a different crease angles for panels, or by shifting the panels themselves a bit. The tutorial is not about that, but solves quite a similar problem: https://boxshot.com/origami/tutorials/mistakes/z-fighting/

Yeah we have to provide our factory instructions how to fold stuff all the time - we just reduce/increase the fold 2-3 degrees.