It would mostly depend on where you are mounting the rad on top of you case. Are you planing on running the hoses out through the top of the case or out the back or side. If you're running them out the top then I would say barbs down. If it's coming out the back then it would depend if the rad is going to over hang the back enough to have the tubes be able to meet the barbs while pointed down or not. The simple answer is that down will allow for a shorter run and less bends in tubes and therefore less chance of kinking the tubes.
If the tubes will be going out the back then you really will need to point the barbs down off the rear of the case.. Otherwise you will have to have them come up and do a loop in order to connect them with the barbs facing up.
If I were doing the same project as you, I would keep everything inside the chassis. put the rad barbs face down through the top of the case then connect the tubes internally to the rad. you would need to cut holes for the barbs but that is not too difficult. Having everything internal will look cleaner and make it easier to move around if needed.
It really doesn't matter which way you position your Rad...Even during the bleeding phase, just tilt the rad left and right slightly to help the trapped air get out, once your loop is fully bleeded, the position won't matters anymore.
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