The potion folmula you have selected is for the potion "Rook", as you can see on the top left of your screen. You can choose to create other potions by clicking on other formulae.
For Rook, only three substances are necessary, you can see what these ingredients are by the little round Icon with the sign in the middle (x, < , >). That is why the other two positions are empty. For more complicated potions these slots will fill up automatically.
To create the potion, you have to click on the create button underneath.
You can also change the ingredients used to create the potion, by replacing them with another ingredient that contains the same substance. For example if you do not want to use your "Diamond Dust" you can replace it with another ingredient, by clicking on the circle with the "x" symbol on the top right of your screen, and see what other alternatives you have.
Maybe alchemy ingredients that are found throughout the world, (Herbalism, Monster Parts, Containers) contain alchemy substances. If you open your Inventory you can see what substances, each ingredient contains.