Best way to keep it cool is to keep it high from the ground and keep your system horizontally. Make sure it's in an open space as well so the fan has proper ventilation. I say keep it high so that various airborne stuff (Dust, pet fur, etc) wont get caught in it. eventually all that stuff stays low to the ground and it'll clog up your system causing it to overheat quicker. Make sure it isn't on a soft cushion like surface either so that any vibration (kids running around, objects falling or giant furniture moving) doesn't jolt anything from the inside, possibly busting up your fan or gpu.
Hope this helps ya.
EDIT: BTW, Never.... NEVER Put a 3rd party cooling fan on your system. it feeds on the power through your 360 and thus actually makes it hotter... And we all know what happens when you overcook your PS3 and 360.