Generally you run the hot fluid to the top so it gets cooled as it goes downward just like the radiator coolant does but it ain't a dealbreaker & especially with 2 coolers there will be some additional routing as you know to connect em up & in your case go with whichever way lets everything connect together the easiest/neatest. On a side note do check that you are getting adequate radiator airflow for adequate cooling at slower speeds in stop & go driving