Top or bottom doesn't really matter as far as performance. Whichever postion allows you the shortest tube length and less severe bends would be the one to go with. Having the barbs at the bottom would make it easier to run a drain tube, which you'll really appreciate later.
You might want to leave your rad unmounted till you get all the air out of your system, that will make it easier to move the rad around and work out the air...EDIT: You do know what I mean go ahead and have everything cut and fitted and all just dont screw it down till the air is out..
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