Hey Robert, no 3D can be visible for the 2D submissions and no 2D can be used for the 3D character itself (anything goes for the 3D entry's background as mentioned in the rules).
As far as your process, you can do whatever you want as long as we don't see it, basically. You can't mix the mediums but you could model something in 3D and use it as ref for your 2D submission, or render a scene and use the lighting as ref, etc. Just the same you might use google to look for refs. It's up to you to decide what you think can you get away with.
As long as the result is that we can't tell, what you do behind the scene is up to you, we can't police it.