Drag a stack of items out of (or into) your inventory (or a container window) and hold the Ctrl key down before dropping to bring up a split stack window, where you can determine how many to move.

For alchemy, you can just drop an entire stack of empty potion bottles on a plant, etc, (one will be used to create a potion and the rest will remain in your inventory) or drag and drop one stack of potions onto another to mix them (health + mana = restoration).