Choosing a wiring color convention might seem unnecessary and may even run counter to the desired asthetic effect for the machine under construction, but we recommend that you adopt a color convention when wiring. It doesn't much matter what you choose, as long as you're consistent. Two that we try to always use are red for positive and black for ground. You always know that a red line has power and shouldn't be connected to just anywhere. We sometimes also adopt other conventions like green for inputs, orange for outputs, etc. The general idea is to use the same color for all wires that do roughly the same thing.
When it comes time to figure-out what is wired to what these conventions will really help.