Hi,
The Freepbx distro uses the *.local of the fail2ban. It means that first the fail2ban reads the regular *.conf files and then the local version of them. So, if you want to add your own version to the fail2ban, add it to the jail.conf file but make sure that it is not similar to the jail.local file to avoid overwritten of the jail's configuration.
You can add your own fop2.conf filter to the the fail2ban's filter directory and add it to your jail configuration.
To check that you have added your jail to the fail2ban, you can type in the linux console iptables -nL and to see all of the fail2ban jails you can type fail2ban-client status.
Thank you,
Daniel Friedman
Trixton LTD.