The ssl certificate for my site https://mysite.mydomain.com will expire in a few day's time and we have a new certificate and key.

How can we change it ?

CA Secure Cloud all versions

The ssl certificate for accessing your Secure Cloud environment is stored in the CA Access Gateway (SPS) component. In particular it corresponds to the ssl certificate for the apache server running in the SPS machine.

There is no specific documentation for doing that, but following the CA SSO guide

https://docops.ca.com/ca-single-sign-on/12-52-sp1/en/configuring/ca-siteminder-sps-configuration/configuring-ssl-for-ca-siteminder-sps/configuring-ssl-on-apache-web-server-manually 

In the part where it references how to manage ssl certificates, it is possible to define and activate for usage a new ssl certificate.