The only section that needs to be removed before adding the add to cart button is the the Form that the Data Assist wizard creates on the results page.
I dont really have a way to troubleshoot the formatting issue you report, I would need to be able to see a before and after copy of the page in the browser in order to tell what CSS is being removed.
see this tutorial for details on creating the catalog:
http://www.webassist.com/tutorials/Create-a-product-catalog-eCommerce-Series
a,d this one for details on adding the add to cart button to the results page:
http://www.webassist.com/tutorials/Add-a-shopping-cart-II-eCommerce-Series