Try measuring how much you need for each wire in the case and trimming to size, it'll keep things a lot neater.
I gather you're testing these things out of the case and that's why you're ending up with loads of excess?
I use a breadboard to test my pedals. I make the board and leave all I/O, pot wires and power connections as flying leads with stripped ends. I connect these to power, a breakout box with a bypass switch and jacks for i/o and to pots via the breadboard (I have a bunch of common value pots with leads tacked to them for testing). So I can test my boards "dry" without soldering them to anything, then when you come to solder them to the case components you can do so "in situ" and get a neater result.
It certainly helps when you get onto more complex stuff