If you are going to use the channels of the extrusions to hid the wires you need to start the wiring very early in the build. Once the wires are installed it is difficult to make small changes to the system without complete disassembly. Putting connectors on each end of the wires can help.
I prefer to use single wires rather than multiconductor cables. This saves a little space and they are easier to route. I did worry too much about labeling the wires. If you have all the motor wires jumbled together, it is easy to sort them out using a meter or power source. I stripped them all then attached about 9V to one wire then touched wires until I heard a motor lock.
I estimated the length of each wire then added about 8 inches. This made sure each wire was long enough for the final dressing and connection.
I tried to add a connector on each side of the wires. That way I could remove a motor or extruder without having to remove wires from the channels.
Female Header - These connectors are used to mate with the RAMPS board.
The Official AMP crimper for these looks like this, The part number is 90418-1. It cost about $100 on eBay, but the Pololu crimper works OK.
Molex Micro-Fit - These are commonly used connectors. I like to use these for the extruder and stepper motors. The pins are rated for 5 Amps each. This is a link to a nice data sheet of the micro-Fit family. http://rhu004.sma-promail.com/SQLImages/kelmscott/Molex/PDF_Images/USA-106.pdf
Crimper: If you want to really splurge on a great tool, buy a crimper. These cost about $140 on eBay. Pololu sells some generic crimpers that do a decent job, but not as perfect as the true Molex crimper. Model: 63811-2800
You can also crimp by simply folding over the flaps one at a time with needle nose pliers.
Extractor: If you want to remove a pin, you can use this tool. It is used to flatten the tangs of the pin so it can be extracted. The pin is destroyed in the process. Here is a data sheet on how to use it. http://www.molex.com/pdm_docs/ats/ATS-011030043.pdf. Molex P/N 11-03-0043
I cut the wires down to about 2-3 inches and attached a Molex 4 pin (2×2) Micro Fit connector. I put the latching side on the motor side because the latch would be on the more accessible side.
This lug is typically used if you want a quick disconnect for the switches.
TE Connectivity 3-520370-2