The conversion guide for customapache (apache 1.3) can be found here: directadmin.com/features.php?id=590
If you're using custombuild (apache 2.2, php5, etc), then the update procedure is:
cd /usr/local/directadmin/custombuild ./build clean ./build update
Then edit your options.conf. Set:
dovecot=yes
save, exit. Type:
./build dovecot
Make sure that dovecot is running. Take a few days to ensure that everything is working correctly. Once satisfied, you can remove the old mbox files by typing:
echo "action=delete&value=mbox" >> /usr/local/directadmin/data/task.queue