IMHO Mail has an unnecessarily complex storage method, not everything neatly combined like some mail clients.
Apple recommends the following:
*To archive a mailbox:*
Select one or more mailboxes to archive.
+Shift-click to select mailboxes that are next to each other in the list, or Command-click to select mailboxes that are not next to one another.+
+Choose Mailbox > Archive Mailbox, or choose Archive Mailbox from the Action pop-up menu (looks like a gear) at the bottom of the sidebar.+
+Choose a folder or create a new folder where you want to store the archives, and then click Choose.+
+Mail archives the mailboxes as .mbox packages. If you’ve already archived a mailbox, Mail does not overwrite the existing file but appends a number to the filename to create a new version of it.+
+If you need to recover messages, you can import an archived .mbox file as ‘Mail for Mac OS X.”+
Normally for a backup you would make a mountable *Carbon Copy* of your whole system from which you can then reimport settings and mail etc as if it was a virtual version of your computer before the reinstall.
http://www.macupdate.com/info.php/id/7032/carbon-copy-cloner (free)
You can compress the archive so it is not as large as the original.
Peter