Depends on the rod, always did vertical for bottom rigs (Penn Senators, Shimano Tiagras, etc...) And across the ceiling with inshore and freshwater stuff.
I'm pretty tall and tend to go higher with storage than most people, just have to keep a step stool around.
Be careful doing the ceiling, don't leave 1oz+ lead anywhere, it'll eventually sag the rod blank, or fall and hit you at some point.