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The interface provided by Windows environment for managing certificates is Microsoft Management Console (MMC). There are three types of stores, user, Equipment and service.
To access .Net web (ASPNET) applications, the certificate must be installed in the Equipment store.
To access.Net Win applications, it is enough to install the certificate in the user store (which is logged at the time of running the application)
The steps for importing a certificate to an Equipment store are fully described below:
1) Get Server certificate
Using the IExplorer, browse the server url (e.g. http://www.domain.com/webservice). Then go to File menu / Properties / Certificates / Details tab / Copy to file and choose e.g. 'Base-64 encoded X.509'. After that you will have a file containing the server certificate.
2) Saving the certificate in an Equipment store
Run from MMC command line and access File/ Add/Remove Snap-in /; Add, click "Certificates" (then computer account, Local computer)
In certificates / click right on Trusted Root Certification Authorities / All tasks / import, and then select the certificate from there
Certificate Store (of import wizard) select Place all certificates in the following store: Trusted Root Certification Authorities.
After installing a certificate you do not need to specify the location of the store.