cPanel offers you a couple options of mailservers to choose from. You can either log into the WHM and pick and choose or do it from the CLI. Both ways are methods are explained below.
Selecting a mailserver through the WHM
First you need to log into the WHM as the user root. Once logged in scroll down the left side navigation until you see the 'Service Configuration' category. From there click on the 'Mailserver Selection' link. You will now be presented with your mail server options. We recommend you choose the default mail server, as of writing this article the default server is dovecot. Select the mail server of choice, scroll down and make sure the convert mailbox format is checked. Click save and the WHM will now install the new server as well as convert your existing mailboxes to the required format!
Selecting a mailserver through the CLI
Log into your servers console as the user root. Once logged in you can run the command '/usr/local/cpanel/scripts/setupmailserver' to see the available options and mailservers you can choose. We recommend you choose the default mail server which at the time of this article is Dovecot. Once you have made your decision run '/usr/local/cpanel/scripts/setupmailserver Dovecot' this will go through and install the mailserver as well as convert any existing mailboxes to the new format.
root@server [~]# /usr/local/cpanel/scripts/setupmailserver Usage: setupmailserver [options] <mailserver> Options: --force Perform conversion even if server is already configured --current Display the currently configured mail server --skip-maildir-conversion Don't convert user maildirs during the server conversion MailServers: courier Standard mail server on cPanel systems dovecot Lower memory usage mail server disabled Disable local POP3 and IMAP functionality root@server [~]# /usr/local/cpanel/scripts/setupmailserver dovecot Configured new mailserver in cpanel.config to dovecot Disabling Chksrvd monitoring Checking that Dovecot is up to date [20131105.170758] Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/i386/rpm.md5 [20131105.170758] Downloading http://httpupdate.cpanel.net/RPM/11.36/centos/5/i386/dovecot-1.2.17-3.cp1136.i386.rpm [20131105.170759] Hooks system enabled [20131105.170759] Checking for and running RPM::Versions 'pre' hooks for any RPMs about to be installed warn [setupmailserver] program "/scripts/predovecotup" is not executable [20131105.170759] All required 'pre' hooks have been run [20131105.170801] Installing new rpms: dovecot-1.2.17-3.cp1136.i386.rpm [20131105.170801] Preparing packages for installation... [20131105.170802] dovecot-1.2.17-3.cp1136 [20131105.170803] Prelinking shared libraries and binaries: /usr/sbin/prelink -av -mR [20131105.170806] Checking for and running RPM::Versions 'post' hooks for any RPMs just installed warn [setupmailserver] program "/scripts/postdovecotup" is not executable [20131105.170806] All required 'post' hooks have been run Converting user maildirs to Dovecot format... Converting /home/user/mail...ok Checking SSL cert...done Checking for expired SSL certs...done Enabling Dovecot in init system Starting Dovecot Enabling chksrvd monitoring Reconfiguring EXIM for new mailserver Restarting EXIM Mailserver conversion complete