When setting up a POP3 account using the automatic or manual account setup, you can choose between creating a separate folder tree in the left pane for your POP3 account, or you can have your items synchronized with the default local folders tree.

Both options will store your emails locally as POP3 accounts do not keep your items synchronized with the server and are only used to download new data. Having the account in the left pane will allow you to move the account in the list of your accounts, having it listed under local folders will, on the other hand, reduce the number of listed accounts.

This choice cannot be changed after the setup, you will need to set up the account anew. Be careful not to accidentally remove your messages when doing so, you can always create both setups at once, copy your messages and then remove the unwanted setup.