Certainly, you can configure your product using our Variants feature:
http://www.e-junkie.com/ej/help.variants.php
In the case you describe, you would only create variant-configuration lines for the particular color-size combinations you actually have for that product.
When you Add or Edit the product in Seller Admin and enable the "Variants having individual price/weight/stock/SKU" setting for that product, on the next screen you can name up to three Options (you will specify only two, named Size and Color), then below that provide a list of every possible combination you will offer, following our standard format of:
SKU,Price,Ounces,Stock,Option1Value,Option2Value,Option3Value
E.g.:
Widget-SmRed,12.95,11.0,25,Small,Red,
Widget-SmGrn,12.95,11.0,23,Small,Green,
Widget-SmBlu,12.95,11.0,31,Small,Blue,
Widget-MdRed,12.95,11.0,25,Medium,Red,
Widget-MdGrn,12.95,11.0,14,Medium,Green,
Widget-MdBlu,12.95,11.0,19,Medium,Blue,
Widget-MdYel,12.95,11.0,8,Medium,Yellow,
(Note here I happened to give every combination the same price and weight, but you can make them different if you wish, and I gave each one a different amount of in-stock inventory units, if you wanted to enable Inventory Control in the cart to avoid selling a sold-out combination. :^)
