ThatOneGuy,
I am sorry to hear that you are having difficulty getting your designs to work in the shopping cart. Without getting down to specifics, I'm not sure what could be causing the trouble.
There is one major difference in the shopping cart code that may be causing you problems and that's because our software is written with the latest version of HTML, also known as XHTML. While the differences are slight, they can cause some unexpected results for those unaware of them. If you go to -
http://w3schools.com/xhtml/ - there are some great references and tutorials that walk you through them. This will not only help you design your e-commerce site the way you want, but will help you code ANY website better in the future.
I hope this helps.