How can I setup a subdomain to be on its own IP on my server? I have configured the server for an additional IP and want to put my subdomain (with ssl) on its own IP. Can it be done?

Yes it can just create an account using the subdomain instead of a domain.

create the subdomain in your name servers zone files.
Then using your control panel add the subdomain as if it were another domain entirely.
once it propagates (eg: ip resolves), it should work.