Speaking as one who does pedalboard design/wiring as a side business (see
instagram.com/dbpedalboards), this is how I approach it:
1) Design the board. Figure out where everything is going ahead of time - both pedals and cable runs. Plan it out with plugs inserted into the pedals so that you know you're giving everything enough space. If you have pedals that you will be interacting with outside of the PBC, then make sure they are located in a place where you can easily hit them. Try not to crowd everything too much - it just makes everything harder, and will give you less flexibility to change things up later.
2) Review your plan. Seriously. You can't spend too much time here. Think through as much of the build as you can and try to anticipate any potential issues - both in the assembly, and things you might not like when you actually start gigging the board. This is why I draw up the boards I design for my customers. I want them to see it and be able to visualize how things will work in the real world.
3) Lock the pedals down. If you're wanting to do a pro level job of this, then use dual lock. It's a lot more expensive, but it locks the pedals down much harder, which will translate to longer cable life, as they won't get flexed by pedal movement nearly as much.
4) Run your cables. You can start running cable from the PBC or from the farthest pedals (I typically start from the PBC), but once you start, stick with it. It keeps everything simpler and more organized when you start locking things down. For the cables themselves, I recommend soldering one end, figuring out exactly what route it will take, then cutting the final length. Give it plenty of slack - cable is cheap, and it can save you a lot of trouble later. I try to keep DC power cable separate from signal cable just on principle, but don't worry too much about it. AC power cable is the real noise source, so it should be kept as far away from signal cable as possible.
5) Lock down the cables. Start from where you've soldered the plugs onto the cables and work your way to the opposite end, locking things down as you go. Take the time to keep it neat. Label everything clearly. Make sure you leave slack on both sides of the cable run, especially if you use plugs that don't have strain relief.
6) Solder on the remaining plug ends. Test each one as you go. It's a hassle, but it can save you a lot of time later.
Obviously there's a lot more to it, but you get better with time and experience. Keep asking questions if you have them, and post pics when you're done!
