Nigel:
You’re going to need to set the full URL of the PDF as the ‘Mouse Click’ URL for whatever element you’d like to open that PDF. It shouldn’t matter much how your PDF is added to your site, but you will need to know the full URL so that clicking on it will open the file.
If the PDF is in your resources library, you can link to it by using this URL:
${resourcesFolderName}/pdffilename.pdf
You may need to uncheck ‘Automatically optimize when exporting’ for that file when selecting in the Resource library. Hype converts single page PDFs to PNGs.