I've never used computer specific fans, so I don't know what the third wire is. Just make sure that they are 12V DC brushless fans.

From a fluid mechanics standpoint, place the fans a the "inlet" forcing air over the amps with a hole at the other end of the rack to act as an outlet. You could place them at the outlet as well. Just remember, if you put one at each end, you will flow half as much air as you would if you put both on one end.

I would recommend that you use either a switch or your amp remote to trigger a relay to power the fans, do not wire them directly to your amp remote unless you want a fried headunit!!