Bert,
I feel for you because we've all been there ourselves. I had many of the same questions, made many mistakes along the way, and have finally gotten pretty good at it. As others have said, follow the rule book, but a lot of it is common sense as well. The trick is having a plan and finding proper ways to support the wire bundles in various locations. Some of the big iron mechanics have access to various parts that make that job easier. For the rest of us, there's always Clickbond fasteners.
Below are a couple of pictures from my Rocket build that have been seen here many times before. They show what is possible with a little pre-planning and patience.
I don't have any special skills and you can achieve results like this. I do have a couple of hints that may make your efforts easier:
1. Have a plan. You don't need formal drawings but you need an idea of what wires need to go where so you can bundle them. Scratch something out that approximates the location of your devices and draw wiring runs between them.
2. I wire from the rear forward. I just got finished wiring my RV-12 which comes with a wiring harness. It goes in just the opposite and boy, was it a pain. Start from the rear, run wires along the path in your drawing and run them to their destination. Leave about 5' tails so you can do the detail routing behind the panel later. Temporarily use plastic wire ties to keep the wires together. Leave them a little loose and you can slip new wires inside them without replacing them.
3. Generally, I like to run two runs through the fuselage. One for power wires and one for sensitive stuff. Keeping these wires apart helps to eliminate noise interference later. It's not absolutely necessary but I like to do it this way. Sensitive stuff would include any audio wires, trim, autopilot, etc.
4. Pay attention to your grounds. Many electrical problems can be tied to bad grounds. Most power components can be grounded at the device, like a mounting screw. I always ground my audio components behind the panel along with the radios so run ground wires back behind the panel. Grounding these locally will create a ground loop which will generate noise in your headsets.
5. Buy good tools and good fittings. Use only airfraft grade PIDG terminals and the proper crimping tool. Same for BNC connectors and pin connectors. Find out the right tool to set them correctly and buy it. Cheapest insurance you will ever buy.
6. Once you get all the wires behind the panel, start organizing them by the device they go to. Get them into bundles as soon as they enter behind the panel. So you'll have a bunch of different bundles entering behind the panel and they need to transition into new bundles for the device that they need to attach to. At this point, you should verify that each device has the proper count of wires for it. Now before you cut any wires, figure out the routing of the bundle behind the panel. Give yourself some slack. Think about removing the device during service or pulling something out from the front of the panel.
7. I like to use wax chord to tie off my wires. I'm not a big fan of the plastic ties although I use them occasionaly. They usually cut my hands when I reach behind the panel so I avoid them if possible.
8. Support for your wire bundles is important. You need to allow some flexibility but you don't want them flopping around. Again, common sense here.
9. There are two kinds of rubber tape that I receommend you purchase. The first one is orange and is very thin. It is latex and only sticks to itself. It is good for wrapping bundles for supporting them. It will protect them from chafing. The other is a black, thicker rubber tape that has adhesive on one side. I use this on any sharp edge close to where my wiring is running. This again puts a rubber cover on a shrp edge and protects my wires.
That's it for now (probably too much). Let me know if I can help with any questions.