Ah thanks. Is there a common way of doing this in a specific order or Do I need to create the email accounts on the new server first before uploading?
No specific order.
And is this the only dir I need?
/var/vmail/vmail1/mydomain.com/p/o/s/postmaster-2014.09.28.13.52.42/Maildir/maildirfolder
Or all of them
/var/vmail/vmail1/mydomain.com/p/o/s/postmaster-2014.09.28.13.52.42/Maildir/.Drafts/maildirfolder
/var/vmail/vmail1/mydomain.com/p/o/s/postmaster-2014.09.28.13.52.42/Maildir/.Junk/maildirfolder
/var/vmail/vmail1/mydomain.com/p/o/s/postmaster-2014.09.28.13.52.42/Maildir/.Sent/maildirfolder
/var/vmail/vmail1/mydomain.com/p/o/s/postmaster-2014.09.28.13.52.42/Maildir/.Trash/maildirfolder
All under /var/vmail/vmail1/mydomain.com/p/o/s/postmaster-2014.09.28.13.52.42/Maildir/.
An easy way is transferring with tool "imapsync", then you don't need to worry about maildir path.