Hello,
Last year we used labeled stickers for our wires, more specifically
http://www.homedepot.com/p/Ideal-Wir...-102/100118882
As for our naming/numbering system, we just started labeling so each 'thread' of connections had a unique number.
It was a bit weird to understand, however, once you get used to numbering system everything makes sense.
Feel free to look at our attached block diagram..