After generating new client certificates from a CA, you will need to install the certificates on the client computers. One way to install the certificate is manually using the graphical interface of the operating system.

The location to install the certificate needs to be in the User's Personal Certificate Store.

If you would like to deploy the certificates through a script you can take advantage of the certutil or Import-PfxCertificate commands. Examples of both commands are listed below:

certutil -f -user -p "password" -importpfx "\\SERVER\share\path\to\certificate.p12"

or

Import-PfxCertificate -CertStoreLocation Cert:\CurrentUser\my -FilePath "\\SERVER\share\path\to\certificate.p12" -Password \$mypwd

Note: both commands needs to run using the user credentials that you would like to install the certificate for. Otherwise the certificates will in the wrong store. For more information please see Microsoft's technet articles on CertUtil and Import-PfxCertificate.