Thanks for the response StopSpazzing.
I have a Linux box here at my house and I tried generating the test certs off-site. I was fine for generating for my actually domain, JetBBS.com and www.JetBBS.com. The problem was with the cPanel stuff. Generating valid SSL certs for stuff like webmail.JetBBS.com, cpanel.JetBBS.com, etc. Those aren't subdomains but VirtualHosts. My understanding was I needed access to the actual document root for those VirtualHosts. For example, if I could successfully create a directory, like acme-challenge and put a test.html file in there, and then successfully view that file by going to something like webmail.JetBBS.com/acme-challenge/test.html, I would of been fine. But because I couldn't do that, I was SOL.
Was I doing something wrong and could I actually of generated valids certs for the cPanel stuff? Thanks!