Option MailDir changes ISPmanager for record in dovecot.conf for new mailboxes line like this:
user@exmple.com:$2a$04$Ei:1001:1002:...m/user/.maildir
You need to configure manually your MTA for store email's in this path in maildir format, for example, changes for Exim MTA
http://forum.ispsystem.com/ru/showthread.php?t=4200