The key to me is making sure you have holes drilled in your benchwork support beams so wires can run in as straight a line as possible from their source to their destination. There are many items which can be mounted on the underside of the plywood (or foam) top of your layout to keep the wires grouped together. You can print out adhesive labels to wrap around each wire to help in easily identifying what they go to. Using different colored wire also helps (say red and black for track power, yellow for switches, white for all lights/buildings, green for accessories, etc.
I'm sure the experts will chime in with more specific and better ideas than mine.
-Greg
