Sadly, it looks like PrimoPDF can't apply a watermark to conversions. A forum post indicated that there's a paid version that does watermarks, but the prices listed at the given links were boggling. Naturally, I thought of the power-packed pdftk, and yes it has that feature.
http://forums.primopdf.com/showthread.php?t=1788
However, the really interesting thing that I stumbled upon was the following post about problems with pdftk for this feature, and how this guy completely figured out what the bug was an how to work around it:
http://rhodesmill.org/brandon/2009/pdf-watermarks-upside-down/
