It's pretty much trial and error. I would do it as follows:
Make sure the two side-lights are exactly the same height as the door
Mull those three together - maybe without casings
Make sure the transom is exactly the same width as the result from step 2
Mull those two together - again, maybe without casings
Add Casings to the final mulled unit
Basically, I don't like the way Chief handles mulled units with casing on individual parts. I find it's usually better to just add the casings, etc to the final mulled object.