What Mr. Wizard says is correct. If you put the knife in “top”, the angle will be slightly lower than in “bottom”.
But the main consideration is that in the bottom position, the knife is usually clamped slightly more securely (hence I usually prefer the bottom position). However, if you put small knives in the bottom position, your stone may hit the clamp while sharpening (unless you increase the angle). So for those knives the top position is often better.
Just give it a try and you’ll see for yourself which position works better for each knife.