Like the other posts said, in theory it doesn't matter where you put your sub, but in reality it does. It matters because of the way we perceive the lower frequency sound and it's not just the physics of things, it's also a psychological reaction of human beings to different sound frequencies. And not just humans, most animals that have a sound sensitivity close to our own.
It may sound like a bunch of BS, but here it is. Higher frequency sounds are attributed in nature as being a disturbance caused by an external influence, like a natural predator, so evolution has forced animals (us included) to learn how to pin-point the location of the higher pitched sounds because that is where the predator is.
This, coupled with the fact that the bass speaker is larger and the treble speaker is very small in comparison, make it harder to pin-point the subwoofer in a system. Sound is actually air vibrating, and the sub vibrates a lot more air then the small speaker does. By the time the sound gets to our ear it has moved a lot in the room, bounced back an forward from many surfaces and has become very uniform and confuses our ears. The small speaker however, has disturbed a lot less air and more of it is reaching our ears directly, and you can tell from what direction it came.
Anyway, we should leave the BS for a moment. I will just share my experience. A sub on the desk is the worst idea. A sub under the desk is a far better idea. But under the desk is not the best location. The best location would be near the corner of the room, a corner formed by two solid walls, and a wooden hard floor. The sub should be positioned directly on the floor (no mats or anything, since they dampen the sound). Everything around a sub will resonate, so you must really experiment which corner is best for you.
It's easy to test, just listen to the sound. If it seems really low, really clean and you feel it more in your gut then in your year then you have a winner. You will see that moving around the room, the sound feels different in all locations. So only test in your usual listening location inside the room. Subs are strange that way, moving them just 10cm in another direction changes the room dynamic.
The more powerful and the more accurate (able to reach a very low frequency response) the less the location is important. But if you have a normal, smaller, computer oriented sub, then location can make it sound like it should've cost three times more or three times less.
