The SiteBuilder is a tool that allows you to create a website. It is, in essence, an HTML editor. You create your page, pick the background color/image, put in your text formatted the way you want it, etc, and it does all of the coding for you.
If you are uploading via FTP, you have to use a different editor or hand-code your page to create it, depending on your preference, then upload it to Verizon's servers via FTP. (FTP stands for File Transfer Protocol.)
If you are just wanting to upload files (pictures, etc) and not create a website, then there is no real difference other than the interface.
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