I am trying to set up email on my web server (FC11) ... I am not new to Linux but am new to setting up email on Linux.

At the moment mail is delivered to:
/var/spool/mail/$USER (single file containing all emails)

Unfortunately I am fairly certain that Dovecot is trying to get the emails from ~/Maildir

Most apps seem to prefer the ~/Maildir method because the files are kept separate so I would like to change from /var/spool/mail/$USER to ~/Maildir.

What do I need to do to make this change for all users? It would be even better if I could preserve the current emails.

I'm not all that experienced with email on Linux either but I believe that you have your concepts mixed up. I have managed email on Solaris and the concepts are the same so I may have some helpful information for you. Let's find out.

Dovecot is a mail transport agent (MTA) or mail server. It should not be looking into the home directory of a user account.

/var/spool/mail/$USER is the correct place for any mail transport agent to work in.

The user account mail in $HOME/Mail is managed by an email client such as Kmail. The email client talks to the MTA. The MTA manages the files going into and out of /var/spool/mail/$USER. The email client manages files going into and out of $HOME/Mail.

I hope this helps.

As far as I understood, ~/Maildir is the preferred place for this nowadays ... can somebody clear this up?

Dovecot needs a folder location and an inbox for the config but /var/spool/mail/$USER is only an inbox.

I am very confused by all of this.