I am not a Brainiac but happy to share my ignorance.
My GRT came with color coded wires for EFIS, EIS (engine indicating system) and some items that interconnect, Autopilot, GPS, Transponder, magnetometer. Cars, motorcycles often have color codes wires, base insulation color, and colored stripe or stripes, etc. Aircraft wires come in any color if that color is WHITE. ha ha. I think you can get TEF Teflon wire in colors other than white but could be expensive way to go. It is not recommend to use car wires for planes, especially in the cockpit due to toxic vapors if the wire torches. You can get away with non TEF aircraft wire under the cowl, like large gage starter or battery cables. Welding wire is often much cheaper.
My intercom came with prewired with harnesses marked. yeah for me.
Large gauge power wires, are fairly easy to mark them. However they are so large and the runs isolated from other wires for the most part, tracing them is easy. Mark away however.
Marking generic white 20/22awg FEP Teflon wire, a little difficult. If you want or really need to mark them, you can....
- Clear heat shrink is your friend. A printer or label maker that can make clear super small font is good.
- Routing in bundles of like function, with good old fashion tracing by your eyeballs and good wire diagram, is easier than one big bundle with many inputs/outputs and functions. Avoid High amp carrying wires bundled with other wires, s/b limited for heat reasons.
- There are snap-on wire markers , plastic rings that have numbers. You can combine them to make some code or unique identifying number. Annotate wire diagram with number code. They come in all sizes even down to 22/20 awg. Not cheap, 300 markers cost $60, 30 of each of the numbers 0 thru 9. You want different sizes. So 3 sets $180? If you mark both ends of wires you may more sets. Do they move around? Can they fall off? Probably not great near heat.
- Color heat shrink tubes, red, blue, green, black. Combos of colors can be coded to mean something. Signal, ground, power.... use your imagination. They will fit on tight but must be slid on before making final connection on wire. Mark your wire diagram accordingly.
Good diagram, grouping or bundling by category of function, no or few labels and tracing wires from/to output/input is time honored, a pain but time honored. Another good thing is access to the wires to start with