Move one of the wires to the center hole that's empty, and leave the one newly emptied hole hanging out over the end of the motherboard connector.
It's easy to move one of those pins. If you look closely at the side of the connector, there's a row of little rectangular plastic "flaps". These lock the pins into the plastic holder.
I use an x-acto razor knife to pry that flap outward slightly until the pin is released. Then it's just a matter of sticking it into the hole you'd rather it be in (don't let it rotate while the pin is out of the connector, it needs to face a certain direction to lock properly into place).
If you have a mobo pin where the now empty connector hole goes, it's fine to be there, it won't mess anything up.
If you need to use that blocked pin for anything, you can carefully slice off the spare third hole from the connector with a razor knife, making it into a two wire connector.
"Most" harddrive LEDs should also work with the SATA channel, though I've heard that some might not. My DFI & Jetway LED's do work correctly with only SATA harddrives in the case.
I don't know much past that.
