if you are using a later version of 2.3 or newer you can do it already. Review the /etc/amportal.conf file and you will find a section identical to below:

...
# The following are used to optionally have the freepbx backup program optionally
# send the generated backup to an ftp server
#
# FTPBACKUP=YES to enable
# FTPUSER, FTPPASSWORD, FTPSERVER must be set
# FTPSUBDIR is an optional subdirectory at the ftp server, it will cause ftp to do a cd
#
# There is no error checking so you should check to make sure these are set correctly. The
# ftp is saved after the backup, so it will not cause the local backup file to be effected
#
# FTPBACKUP=yes
#FTPUSER=asterisk
#FTPPASSWORD=password
#FTPSUBDIR=mybackupfolder
#FTPSERVER=myftpserver

# SSH BACKUP INFO: must have a valid SSHRSAKEY file and server, only supported through
# ssh. SUBDIR is optional and will be created if it does not exist.
#
# If SSHUSER is not set, it will default to the current user which is asterisk in any
# standard configuration.
#
#SSHBACKUP=yes
#SSHUSER=backups
#SSHRSAKEY=/etc/asterisk/backup_rsa
#SSHSUBDIR=mysubdir
#SSHSERVER=mybackupserver.com

# AMPPROVROOT=/var/ftp /tftpboot
# One or more directories where there are provisioning files that should be included in the backup. Currently
# these get backed up only, the FreePBX utility does not automatically restore them.
#AMPPROVROOT=/var/ftp /tftpboot
#
# AMPPROVEXCLUDE=/var/ftp/exclude-from-file-list
# a list of files to exclude, to be used in tar's --exclude-from argument
#
#AMPPROVEXCLUDE=/var/ftp/exclude-from-file-list
...

Note the AMPPROVROOT variable. Add those directories that you want backed up and it will back them up.

I personally backup /tftpboot as that's where our phone configs are. along with that one I have added several other directories that are not normally included just in case. (system will only crash and need to be rebuilt when I'm across country on vacation). Some if the others are: /var/lib/asterisk/bin, /var/lib/asterisk/agi-bin as I have customized some scripts in those. /var/lib/asterisk/mohmp3/ for the reason you want it. /var/www/panel as I've tweaked the panel for 60 extensions and over 25 trunks. /etc/hosts /etc/resolv.conf /etc/logrotate.d/asterisk (I have tweaked the log rotate schedules) and that way I can get restored quickly without having to find my written notes and retype things.