Copy the PDF into the K4PC folder, which is "My Documents\My Kindle Content".
Calibre can manage K4PC ebooks (import from the K4PC folder, export to the K4PC folder). Use MOBI as the output format for the Kindle.
Many ebooks have DRM (encryption), Calibre can manage DRM-ridden ebooks but can't convert them to other formats. It is easy to strip Amazon and Adobe DRM, see Apprentice Alf's Blog for more about DRM and Calibre.