Hello, not quite sure what you’re referring to, are you setting up a new POP3 account in eM Client? If you’re referring to setting up the account in a local folder or a separate folder tree for the account, the difference is in listing the account and folders which will receive new mail.
eM Client by default includes a local folder structure (note that POP3 account do not backward sync to the server), you can either sync your server content with the default local folders or let the application create a separate folder tree for this account only - essentially the behaviour is same, but if you’re using multiple POP3 accounts, you might prefer to have the account stored separately in it’s own folder tree.
Regards,