Q.
I'm installing crown moulding in rooms with cathedral ceilings, some square and some with jogs.
Do you use the ceiling as the reference plane and have the rake moulding at a lower angle, so you'll stay at the same angle relative to the ceiling?
Or, do you use a transition piece where the wall meets the rake?
The toughest cut is where the level ceiling meets the gable (or rake) at an inside corner. If what you're referring to is where a level portion of the ceiling meets the rake (forming a compound miter), that is somewhat easier.
I don't bother with complex mathematical solutions; an old carpenters' trick works best for me. Take two scrap pieces of moulding, tacking one to the level plane, as it is to be installed. Then take another and, having tacked it to the rake, allow it to overlap the piece on the level, drawing a visual line from where the top edges intersect to where the bottom edges intersect.
With a handsaw, cut through the two pieces forming the compound miter. You can then fine tune the cuts on a compound miter saw, noting the degrees for the rest of the room. Many, many old homes with Yankee gutters formed from tin in back of crown moulding were cut using this method, where the gable or rake moulding met with the fascia moulding.
It's a little tricky at first but with a little practice the time it saves is well worth it.