You don't say how big the bear can is, or how heavy.
What really matters when loading a pack is weight distribution. Generally, you want the greatest density both low and close to your body, where it puts the least strain on your back. If the food is the heaviest thing you're carrying, you probably want it at the bottom! On the other hand, if the bear can is mostly empty, you probably don't want it down there. That's especially an issue later in the trip, because the bear can will weigh less each day.
I frequently end up with the can vertical in the middle, right above my sleeping bag, with other stuff shoved in on either side. That, or my son is carrying the can!
There's really no good answer when it comes to carrying big items in a pack. Our packs generally weren't designed for that. Maybe manufacturers will start taking the trend towards requiring bear cans into account, eventually.