It depends. If, for example, you had put it in a drawer, or a bin, or some type of container, you'd say "in the bottom." If you'd set it on a shelf or in a stack of items on the floor, you'd say "on the bottom."
"Where did you put my stapler?"
"It's in the bottom drawer of my desk."
"Where did you put that latest shipment of nails?"
"Aisle three, on the bottom shelf, just to the left of the claw hammers."