If you look at the "weapon stores a spell" part of the item wizard, there is a box called "charges". If the player runs out of charges he cannot use the weapon, no matter how many bottles he has left.

And another thing; when the spell is cast, the player will have to click on the moster that he wants to throw the bottle on. When a spell is cast, it is cast as if the player had cast it himself, which means that penalites apply, and he will also run to the target.