Thanks everyone for your help!
What we are trying to accomplish is the following. We are implementing a sercure payment gateway with a 3rd Party Bank for e-payments. We have proviced them with our Public key and we have our private. The issue we are having is that we dont want to run the website under the default "Local Account" assigned by the Certificas MMC snap-in when importing the certificate. We want to import the Certificate using the option of Network Services and configure a Application Pool to use under the Identity the Network Service Account, which rigth now this Network Service Account is not able to access the Certificate since its located under Certificates | Local Computer | Personal | Certificates.
Hope you can understand my situation.