Well, make an item called 'Empty Bottle', problem solved.
Now onto the next bit. Your best bet is just to use Conditional Branches.
Example;
@>Conditional Branch: [Empty Bottle] in inventory
@>(What you want to happen when you've got an empty bottle, e.g. fill it up)
: Else
@>(What you want to happen when you've NOT got an empty bottle, e.g. nothing?)
That could be an event for a single-use empty bottle...Unless, not sure this'll work, but you could set up a common event so that when you use the potion, it removes the potion (obviously) and gives you an empty bottle back.
Example;
Set the common event on the potion item (under Database) to 001: Empty Bottle, then make the common event add an empty bottle to the player's inventory.
Hope that helped...If it's wrong, it's because I'm rusty.
Good luck.