I have a site that I am transferring from my old host to my new server. This site already has SSL established and I have been given the key pairs which I am going to try and install so I don't have to buy a new SSL for this client (has been successful before).
My problem is... their SSL is not on a subdomain. Thier SSL is setup like: https://domain.com
Obviously, I know how ot setup an SSL like: https://sub.domain.com but I am running into issues as to how I logically do it without a subdomain.
Your directory structure would be identical to your non-secure portions. To use a cert, you need to call pages (and any files in it) through the cert. In your case, let's say you have a directory "page", in the root. To call a file from there non-securely, use 'http://domain.com/page/filename.htm'. To do so securely, just add the "s" to the http. 'https//domain.com/page/filename.htm'.
In the same directory, but called "through" the cert.
On these other hosts, were you using their cert, or your own? It's possible they were using a server wide cert, and had the 'secure' directory symlinked or aliased (the precise method I don't know) to pass through their cert. I think Plesk servers commonly use a 'secure' directory, IIRC.
Secure? Yes, as long as it passes through the cert, it should be encrypted between the user and the server. What happens to the data afterwards is another matter.