I'm not sure about how the server end of things works. I use my web-host for email.

On the client end, when you set up the accounts in Thunderbird, you can choose to use POP3 or IMAP. From there, you just have to enter the right info.

I originally started using IMAP so I could keep all my machines synced. Mark a message read on one machine and it shows as read on all of them, for example. The one pitfall is that if you delete a message on one machine, it deletes it from the server. I get around that by having my POP3 machines set to check email every 5 minutes and download a copy of anything new.