The trains that split apart or join always have one segment with the sleepers at the front (hopefully behind a baggage car to reduce the noise) and the other segment with the sleepers at the back. This way, when joined up, none of the coach passengers have to walk through the sleepers to get to the diner, cafe or lounge car. If each segment has a baggage car, it has to be in front of the sleepers (right behind the engine) on one segment and at the very end (behind the last sleeper on the other) because if one ended up in the middle, passengers wouldn't be allowed to walk through it. This definitely applies to the LSL and the EB. It is possible they actually reverse the direction of the TE/SSL when they join them up, so the two separate trains have the sleepers at the front, but then the back of the TE joins to the back of the SSL and travels backwards to LA? Maybe? I was asleep when this happened and didn't notice the one time I took the TE from Chicago to Tucson, but I got this impression from some post here. Or maybe that was an odd thing that only happened once.
They could in theory rearrange the trains when they combine, but that would take a long time so they never would do that unless they had to remove a broken car from the consist. Then, I'm sure, they would do the minimum possible switching.