After a very long pause, I am returning to this amazing game! However, I can't remember if there's a way to split stacks. When I threw some empty flasks on the mushrooms, I got one potion, but the rest of the flasks disappeared.
To split a stack, hold down control and drag the stack onto the ground or into any container. Only one bottle is used when creating a potion, the others may be covered by other things in the inventory, making them invisible.