Drag and drop the entire stack of empty potion bottles onto a plant; only one will be used, and the rest will remain in your inventory. Same for mixing health and mana potions to make
restoration potions.
Make sure you are standing close enough to the plant that it is highlighted in white when you mouse over it, rather than red.
To split a stack, though, drag it into, out of, or between your inventory / container / ground, hold Control and drop; this will open a 'split stack' window, allowing you to select how many to transfer.
