what's the difference

[qwex]

my swiftech mc462 is in (hopefully correctly) but there are two cables coming out - one is 3 pins, for the motherboard fan header. the second is full sized (like the one the hard drive uses), I guess 4 pin, but only 2 pins are actually in it. which one do I use, or do I use both? right now I'm thinking the 4 pin sized one (with 2 pins) is for power, the 3 pin is for measuring fan rpm, but I wanted to make sure.

thanks in advance