Unfortunately by default a RoundCube installation is not going to be able to manage cPanel e-mail account credentials or any e-mail filters, and these would need to be managed via cPanel directly.
I believe there is a cPanel password plugin for RoundCube that might possibly function, but it's hard to tell if it has kept up to date with recent cPanel updates. You should have a /plugins/password/config.inc.php.dist configuration file where you installed RoundCube, and it should have a option to change the $rcmail_config['password_driver'] option from sql to cpanel.
Further down in that configuration file there is then a cPanel Driver options section that you would need to update. Then you would need to name the file config.inc.php to make it active. You would also want to ensure that you have that plugin loaded in your main RoundCube configuration located at /config/main.inc.php by having the following line:
$rcmail_config['plugins'] = array('password');
Even if that works, e-mail filters would still need to be done directly through cPanel. So you might also simply think about educating your users that cPanel is used for managing their e-mail account and setting up filters, and your custom install of RoundCube is for simply checking the mail accounts themselves.
Please let us know if you have any other questions at all.
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