I’ve seen the undersides of a lot of layouts, and the one thing that’s held true for all of them is that the ones with neat wiring were the most reliable. I use barrier terminal strips, wire anchors, and wire ties to keep my wiring organised. Not only does organised wiring help with layout reliability, it’s also easily traced, which helps you debug problems quickly.
Keeping a logbook with diagrams and notes about your layout wiring is another good idea. This will help you decipher your own wiring practices when looking for electrical problems.
One of the best practices is to use color codes, which creates self-documenting wiring. On my layout, I use black and red wires for track power buses and feeders. If you have places where track buses from multiple power districts are in close proximity, you might consider using different colors for each bus to keep them straight.