Black is very likely to be the minus side. Red and yellow are probably the 5 and 12V, but which is which could definitely go either way. You do want to be sure you use the right one, because you can actually burn out a motor by using too low a voltage.
If it's a 12V pump, and your supply gives 12V and 5V, why not just try it on each wire (for a couple seconds) and see which one runs the pump faster?
As for what to do with the other wires, maybe trim the shield back as far as you strip off the outer insulation, then let the unused wire go another half inch or so. The two wires you're using can extend out beyond that to the pump, and you can wrap the whole thing with tape. There are better-looking ways to do it, but this will be more than enough for low voltage DC.