The proper way to add metadata to a PDF would be through XMP. It allows you to add arbitrary metadata and allows defining the metadata types inside of the same PDF file (which you really should do if you're archiving and which is a requirement in archival standards such as PDF/A).
XMP data can be extracted by readers who don't understand the PDF format using a simple text scanning algorithm yet at the same time it will be inside of the document so will be protected by the digital signature you apply.
You can read more about it here: http://www.adobe.com/products/xmp/