Stack to a higher number is good, but I wont want them to be on the bottom.
I like my consumables either at top or bottom so I can get to them quickly. Personally, I feel it's easier to go all the way to the bottom is easier than stopping exactly somewhere down the middle (and that somewhere changes as the cult rune stacks grow would be more annoying)
On a side note, I don't have nearly as many stacks since I decided to max cult all my ninjas...