now need to do the same with FM on the same server
FM is the client tool. I wouldn't know about installing it on the server.
To simplify my user experience, I have FM installed 3 times on my workstation -- once for each environment. That way I'm not always opening Cognos Configuration. The good news here: Once I had my Dev install configured to use SSL, I copied the install for QA and Production, opened Cognos Configuration once (each) to change which server it pointed to, and I was done. It works because the SSL cert is for the client machine. Plus, by copying rather than installing again, I didn't get a new INSTALLID.
I have instructions, but they are probably customized to my environment. They are on an internal wiki. A simple copy-paste into this forum probably won't work well. Basically, follow IBM's instructions regarding the process and using ThirdPartyCertificateTool.