You can upload your PDF file through the Images -> Upload an Image function to get your file onto the server. However you cannot select that file as an image setting for a ShopSite page or product, these settings should only be used with actual images because the HTML to put an image on a page is different than what you would need to link to some other kind of file, such as a PDF file. You would have to create the HTML for the link yourself and put that in one of the text fields (for example, if it is for a product, you could put the HTML link in the Product Description field and/or the More Information Page Text field). If you upload through ShopSite's Images function, then the file is always going to be somewhere with the 'media' subdirectory of the directory where your ShopSite-generated pages are. So if your ShopSite pages are at:
http://www.yourdomain.com/store
then your file uploaded through the Images menu may be at something like this:
http://www.yourdomain.com/store/media/yourfile.pdf
In which case the HTML for your link to this file could look something like this:
<a href="http://www.yourdomain.com/store/media/yourfile.pdf">Download the PDF File</a>
The the text 'Download the PDF File' that would be on your HTML page would then be a link to the file you uploaded.
-Loren