Here is the documentation on how to add attributes / combinations to a product in PrestaShop -> http://doc.prestashop.com/display/PS16/Managing+Product+Attributes
If you plan on using multiple attributes for a product, like size and colour, do use the combinations generator and select both the possible sizes and colours at the same time. If you add them by hand one by one you risk ending up with a scenario where only the first attribute is visible in the shopping cart and on the resulting order (like the size but not the colour), i.e. you will have to contact the customer to ask about the other attribute(s).
By using the generator PretaShop will create the all the necessary combinations for you, i.e. size 1 + colour 1, size 2 + colour 1, size 1 + colour 2, size 2+ colour 2 and so on.