Cyrus uses a combination database index as well as file structure where each file is an email message. The Cyrus database format can be a variety of formats: skiplist, bdb, etc. In addition to the individual account database information (which can be used to reconstruct mailboxes), there is also a listing of which accounts live on which server in a multiple server/clustered IMAP server environment. If you are using a new version of Cyrus, you can work with a unified murder server/IMAP backend environment. I'm assuming that none of this applies to you really if your OS X Server is your only IMAP server, but you may have stumbled across these configurations.
I would be surprised if Apple touched the Cyrus source code at all, as Cyrus runs a lot of big enterprise email systems. They may have provided their own GUI for cyradm (the CLI admin interface), but that's about it. Therefore, you should be able to get all the help you need in the general Cyrus community.