Single freepbx designed to work with
1) single /etc/asterisk and /var/lib/asterisk/agi-bin/, /var/lib/asterisk/sounds/ folders and astdb at /var/lib/asterisk/astdb
2) single asterisk instance controlled via manager interface.
You can use more then 1 asterisk, but you will loose ability to call from one asterisk to other(without REALLY HUGE rewrite), also you need ensure you synced astdb and folders and reloaded second instance yourself.
For run second asterisk instance you have use -C param when starting asterisk, after that in asterisk.conf file supplied in that param supply other dir with OTHER ports for sip,iax,manager( two modules of different asterisks can't work on same port).
Correct setup for load balancing is use of kamailio+ multiple asterisk. But you have understand what you are dooing and most freepbx features will require rewrite.
So if you ever expected go over 500 calls, i can recommend you get rid of asterisk and request someone write special dialplan just for your need.