1. Make a copy of cgminer.sh before you install bertmod in your /config directory. Use that to modify and stop and start the miner.
2. Don't use Bertmod for bfgminer, use the latest firmware from KnC it has bertmod installed.
3. You will need to search for a modified cgminer.sh to use after you installed the latest firmware, it works with both cgminer or bfgminer to add back the overclocking parts of the script. There are a few floating around in this thread I believe