This plugin allows your users to cypher a folder at the root of their repository, using the underlying EncFS mounting. It thus requires a filesystem as driver, and encfs installed on it. You must also make sure that the www user will have the right to execute the encfs and encfsctl command, use SUDO for this, for example
www-data ALL = NOPASSWD: /usr/bin/encfs,/usr/bin/encfsctl
In order to be able to execute the encfs commands in a totally non-interactive way, you must generate a template file called .encfs6.xml before using the plugin. See the instructions below.

Once installed (see http://www.arg0.net/encfsintro), simply use the standard encfs command to create an encrypted folder :
encfs ~/.crypt-raw ~/crypt
Follow the instructions and choose how the filesystem will be encrypted, and set a simple password. Do not bother about this password strength, it will be changed anyway when the user will actually cypher its own folder. Simply remember it. Once this is done, you can find inside the /.crypt-raw/ folder an .encfs6.xml file.
Use the full path to this file, along with your simple password, as parameters for the cypher.encfs plugin in the Pydio GUI.