You shouldn't embed PDF's on your website. Forcing users to browse PDF files makes usability approximately 300% worse compared to HTML pages. PDF is great for distributing documents that need to be printed. But that is all it's good for. No matter how tempting it might be, you should never use PDF for content that you expect users to read online. Using one of those stupid flash thingies to avoid embeding PDF's, but for the same purpose (displaying an embeded document) not only is still bad, it is in fact worse.
More info about this here.