Being an electrical engineer, I suggest you start by developing your wiring diagram on paper. Figure out what you are going to need to wire (avionics LRUs, lights, AP servos, switches, alternator(s), master relay, starter relay, battery, sensors, etc, and then put each on your diagram. Then start adding the interconnecting wires to the diagram, and label each wire with a unique wire number and wire size. Once you have your wiring diagram complete, you can then figure out what your wiring harnesses need to look like, how many wires go to each part of your aircraft, etc.
Some people have used a wiring schedule/table that has the same info on it, building it in a large spreadsheet. This can also work, but I personally find it harder to read/understand than a wiring diagram.
If you just start running wires without a well thought out plan (in the form of a wiring diagram), you will likely end up with your dreaded spaghetti bowl.
Regards,