There is a way to create items with different values for each attributes and having their own stock level:

Go to the Product List and select a product (this becomes the parent product then).
Now click "Add attribute" in the toolbar. It should redirect you to the attribute form.
After you have added your attributes (say: "Size" and "Color"), you must go back to that product which now has attributes added to it.
Now click "Add items" in the toolbar to add child products to this product. You must now give those products values for each attribute "big" and "green" is an example. Those products have their own stock level now.

Currently child products can't be assigned to another parent product, but it is surely a good way to control your stock.