I start by laying the harness out and grouping the circuits together such as dash,rear of car,engine bay,etc. I'll then take a few small wire ties to hold each group together. Decide where to mount the fuse box and then start laying out your groups to where they go,planing the routing & mounting as you go. Once you get your groups in their general locations I like to wrap each group with good quality electrical tape sorta like an OEM harness,but leaving plenty of wire out the ends as you can finish wraping later. I like to start at the dash and column first,one circuit at a time, cutting to length, and connecting permanantley using solder and heat shrink,"never ever use crimp connecters"
Main thing is you don't want any dangling wires or extra wire that you have to roll up,everything should be nice and neat and as short as possible. You may very well have some extra circuits that will not be used at this time such as map lights,air conditioner,etc, with those its a good idea to roll them up and hide them behind a kick panel or such in case you want to use them at a later time. Don't forget about grounds, on a steel car you'll need battery to engine,engine to chassis,engine to body. On a glass car you'll need battery to engine,engine to chassis,and every componet mounted to fiberglass will reguire a ground to engine or chassis. Hope this helps ya. Just take your time and plan it out,you'll do fine.