the process depends if you are changing the cert on the gw or on the management server. if you are changing the cert on the gw , another question raise , do you have other portals running like Mobile access, captive portal, usercheck, etc.
On the gw, if you have multi portal daemon running you have to do it from smartconsole. if you don't have multi-portal daemon you have to follow the provided Sk.
In order to use the certificate you have to generate a csr. you generate csr from any Linux or windows machine and sent it to the CA to sign it.
Based on your description, you want to change the gaia portal cert with your CA cert. You are mixing 2 things the server certificate and the signing certificate and they are different. Gaia uses server certificate.