think I recognize this question from the oscommerce forum ;).
…and still not sure what you want, but cs-cart looks flexible with options. In the trial version you can set all kinds of options, have you tried? What is it that doesn’t work?
this cart does have the ability to add optons to the products, when you are in the add product part look at the tabs and youll see product options. go in there and check that part out, i have added colors and others have added sizes and such, there is a part that you can add a text box or an input text or something like that. im not sure how it would excactly work for your embroidery but play with it, and see what you can do