The most important element of your cert is that you use a hostname (common name in SSL terms) that resolves publicy and internally.
Typical hostnames are:
mail.mydomain.com
domain.com
server.domain.com
That hostname should map to the public IP of your server (when looked up externally) and should map to the LAN address of your server when looked up from your LAN.
Here's an overview to get the process started
Go here

Chooe Manage Certificates (this gets you to the section where you can create a new cert)

Create a new cert (for now, this will be a self-signed cert)

Enter the name, this is IMPORTANT
It must be the hostname you will use to access the server
(mail.domain.com, domain.com, etc)
The other fields are not important for the typical server (but feel free to explore)
Click Create

Now you will see the new certificate in the list.
You need a CSR to pass to your SSL provider, choose this option

Here's what the CSR looks like.. Copy it and use it during the SSL ordering process with your provider.

Your SSL provider will verify that you are associated with this domain, when done they will return a 'signed certificate'
You then choose the option above to 'Replace Certificate with Signed or Renwed Certiciate'.
When you choose that option, you can include the intermediate certificate, for example, godaddy always gives you a cert name 'gd_intermediate.crt) which you need to include.
I hope that overview helps
Jeff