If you have other mail clients which access your mail with POP, remove the POP configuration on them also. You should access your mail only with IMAP-based clients. You can have other mail folders on the server also. If you don't tell your mail client where to store the mail folders, they'll go in your UNIX home directory. When you access a folder, the server reads the entire file into memory.
Big folders can take a long time to open.
The IMAP server uses mbox-style folders by default, but it can read and write other formats. After you get your client configured to look in a particular subdirectory for your IMAP mail folders, copy your other UNIX-mail folders into that directory. That is, in the default configuration the server does not support folders which contain both messages and subfolders. If your mail client has a setting for this option, be sure to set it appropriately. You will then be able to create sub-folders under that folder.