There are 2 basic ways to use ShopSite,
1. Create all your page and product content in ShopSite and have ShopSite publish your pages to the web. ShopSite will put the pages on the web at the location specified in the url in the authorization file that your store runs from.
2. Create all your pages manually (or with some non-ShopSite tool like frontpage) and include the product description graphic etc on thoes pages. You also enter your product name, sku and price into ShopSite and then copy the Add to Cart and View cart links from ShopSite to the pages your manually create. This is called the Order Anywhere method.
From what you are describing it sounds like you are using the Order Anywhere method. Is that correct?
If you are using the Order Anywhere method there is no need to use the Publish option in the ShopSite merchant interface (backoffice) since your pages will be created outside of ShopSite. All you need to do is enter the Product information including just the Name, Price (and SKU if you use one) for each product you will be selling. Once that information is entered, in the backoffice of your store you go to Merchandising > Order Anywhere and select each product from the list. Depending on the software you are using to create your pages you may want to either Show Selected Links or Show Selected HTML buttons to display the buttons or html to add your products to the cart. If your browser and page creation software support drag and drop you can use the Show Selected Links method to display the buttons and drag them to your page. Otherwise use the Show Selected HTML and copy and paste the html to your page. Once you have your pages created manually you will need to ftp them to your your online store.