I am going to add shared ssl to my server using the https://server1.domain.com/~user method. I have read a bunch of posts but I still have one question. I have my server named my.domain.com but also have registered securedomain.com and want to use it for ssl. Can I just point the secure domain name to the main server IP or will I have to change the server name?
I'd create a seperate account with a dedicated IP for securedomain.com on that server. If you're using CPanel, it should automatically add "UserDir public_html" to that domain's <VirtualHost> block, meaning things will begin working as soon as you generate the CSR and install the dummy cert.