Make sure to plan ahead in wiring as far as layout goes. We usually get to know what all we need to wire to and where our limits are so we get to work with all of our components on our base board knowing where they would best fit. We also make a digital schematic with all of the parts showing wire connections to what and where they go to. Make sure you keep in mind where mechanical or pneumatic stuff needs to go.
As far as keeping it organized on there, we use
wire spiral wrap to keep groups of wires together or the wire ducting/highways. You can use zip ties for situations you might need as well, such as if you have one going a long way around your robot.