Off-board wiring doesn't have to be a mess. As BTR says it pays to keep the wire as short as possible. But I also think it's important to make it logical so that trouble shooting is easier. Colour coding is a very good idea.
There is a logic to populating the interior of the box. I like to put the stomp switch, DC socket and pots in first and get them all wired up first - ground wires, Volume pot 2 to Out, that stuff. Then I install the jack sockets because most of my pedals have top-mounted jacks these days and they can get in the way of the pot wiring. I like to route this wiring around the perimeter of the enclosure, which makes it neat, keeps it out of the way of the circuit which may help to keep it quiet, and avoids it getting trapped under pots.
Which only leaves wiring the board in place. As I add the wires to the board I kinda put the board where it will sit, pull the wire to the pot where it will connect and cut to length. That means there is only enough wire to join the board neatly to the necessary connections and no more. It actually doesn't take any longer now that I am used to it and not only is it neat it helps keep the board in place. If I want to make changes later on down the track I can usually just unbolt the lower pots and I can get access to the underside of the board.
I guess it's because I came to building pedals from building amps where lead dress is extremely important that I do it this way. Building amps is all about off-board wiring!
Here is a recent build. You can see that the in and out wires to the jacks go around the outside of the box, hopefully avoiding any chance of interference from the circuit. In most pedals its not really an issue but I think it's good practice to avoid any problems you might have with higher gain circuits or whatever. For the same reason the wire from pin 2 of the Volume pot goes down the middle, away from the pedal's output wire. Over-cautious for sure! You might also make out that the wiring from the board to the pots is only just long enough. There is plenty of wiggle room really, but not an excess of wire. In general these pedals are very quiet. Maybe that's more down to the low gain of my preferred pedals I don't know, but less wire can't hurt.
Oh, and I do like to sand the edges of the board flat after cutting just as BTR describes. I have a belt sander so it takes all of 30 seconds to do. It stops wires getting caught on the edge of the board.
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