I read that it really doesn't matter but in on the top has its advantages (flow/gravity/air pockets).
I can suggest a SLOW fill with the IC being the highest point. Seems some guys had trouble with air pockets when filling. If the fill rate is slow enough, air will be displaced as the fluid rises without trapping an air pocket.
Ya, instead of filling the upper IC i tried something new...I took the lines off and filled them untill both where full. Now i'll connect them to upper IC and fill it with pump running...See if that is better than just fill upper IC?