The only thing that really matters much is to have the pump after the resevoir (and below it helps too). This is more to facilitate filling and bleeding the loop, but also to help the pump get as much water as it needs. Restriction on the pump inlet is bad for performance.
As for the radiator, if the radiator is in the top you can get air bubbles in it, but all you have to do is tilt the case around a few times to get the air out, so it isn't really an issue.