Hi,
You can use NCryptoki to sign a PDF but, explain here how to sign a PDF by using NCryptoki is a bit hard. There are a lot of things to explain, from the PKCS#7 format to the PDF signature format (PAdES).
You can avoid from all this technical stuffs by using my NDigitSign library. By NDigitSign you can sign a PDF file in the standard PDF signature format (PAdES).
You can download the latest version of NDigitSign from the download section.
In the zip file you can find also an example on how to sign a pdf.
If you need help don't hesitate to write me (see in Contacts)
Regards,
Ugo Chirico