You can either roll a solution yourself or use an off the shelf solution such as the CoSign Central digital signature appliance from DocuSign (my company)
Note that if you decide to roll your own solution, you must ensure that the signer has sole control over their private key. (Presumably what is included on the CDs that you received.)
This is another aspect of using a SSCD (Secure Signature Creation Device) for creating the signature.
Bottom line: for using X.509 digital certificates to digitally sign documents on behalf of person, the entire system must meet the legal requirements for a digital signature system (US terminology). In Europe and elsewhere, this called an Advanced or Qualified Electronic Signature system, depending on the source of the root cert of the signer's cert.
This is different than code signing, signing SSL requests and other uses of X.509 digital certificates.