I went from what the default ISPC2 Perfect Install used to the ISPC3 Perfect Install's defaults.
I know there was a change in ISPC2 from mbox as I recall.
Then, on my upgrade to ISPC3 I moved the mail over.
My ISPC3 settings show: courier and maildrop.
I didn't use anything special to migrate. I had an old forum post where I was told to copy to the vmail. Per Till: "Recreate the mail accounts in ispconfig 3 on the new server. Then copy the content of the "Maildir" directory on the old server to the corresponding directory /var/vmail/domain.tld/user/ on the new server. Then chown the data to user and group vmail."
ISPC3 on Debian! It's great!