Lessons I've learned from darkrooms I've worked in or put together:
When you decide where you are going to put safelights and regular lights, make sure that you don't end up with a situation where your own shadow falls on the working area.
When you design your area for trays, be sure to include space to empty the trays easily.
Remember to include a dry area for a paper cutter and one or more paper safes/drawers.
Lots of electrical outlets, spread over more than one circuit.
Separate the safelight and regular light switches.
A floor that will withstand spills and is easy to clean.