Align the driver to the driven. If you rotate a command module so the ladder aligns with the lower sections you will hate yourself when you try to use the directional controls. It also makes space hangar part alignment impossible.
Do not save the last bit of staging to detach in final re-entry in an attempt to limit space debris. It works fine *most* of the time but can also come back and hit you, or even worse, clip into the heat shield and make the craft uncontrollable.