Yes, the shopping cart can be used with an existing site or standalone. There are 3 main methods of adding the cart with an existing site.
1. Add a link to the existing site that says something like "Click here to shop now" or "Shop Now" and link it to the cart. This is the easiest and usually the first step most new merchants take.
2. Link from existing product or department pages to the relevant page in the cart. For instance a product information page could link to the item detail page in the store with the add to cart button. Or a department page could link to the individual item pages.
3. Add "Add to Cart" buttons to the existing site. In the item edit screen there is an add to cart snippet html code which can be copied and pasted anywhere. This method can be very labor intensive especially for stores with large amounts of inventory.
Most merchants move the entire site over to the store builder to save on costs and for ease of maintenance. Existing html files can be uploaded directly to the store builder and used as before or the content from existing pages can be added to the store builders "pages" from "Design-->Pages" and the design can be modified to match the existing look and feel.