You will need turn off fetchmail, then delete your present mail store (or at least rename the directory to take it out of circulaton), then edit .muttrc, .fetchmailrc, and .procmailrc to reflect the new configuration. Then turn fetchmail back on and test.
Note that, if you are using the mbox format, the mail does not go into subdirectories of the Mail director in your home directory. It goes into files (called "spoolfiles") in the Mail in your home directory, except for any mail that you choose to leave in the default mail directory of /var/spool/mail/[username].
This web page will provide far better guidance than I can, as it describes setting up an mbox style mailbox. http://docs.huihoo.com/gentoo/resour...e-to-mutt.html
It was a primary resource when I set up Mutt for the first time.
I'll give you some sample lines from my .muttrc indicating where you should look to make your edits:
In addition, any mailboxes configured in .muttrc will need to be edited appropriately.
In .procmailrc, you will need to edit the mailbox type. Again, some sample lines:
You will also need to change any recipes in .procmailrc to reflect the new configuration so that they point to the spool files, rather than to mail directories, as well as create the spoolfiles for any mailboxes you want in addition to the main one in /var/spool/mail/[username].
I did a podcast for Hacker Public Radio
about setting up Mutt. You may find some of the links in the shownotes helpful.
(Two years ago, before I decided to Mutt, I wouldn't have understood a word of this.)