philologic.cfg lives in the /etc/philologic directory (TODO: is this configurable?) and controls a number of global configurations options for Philologic. Contrast this with philo-db.cfg, which lives in the individual database's /lib directory, and sets varibales on a per-database basis. Some of the variables in philologic.cfg can be overridden in philo-db.cfg.
This file is fairly well commented, so you should be able to read through and get enough information to make informed changes.
Some of the variables here can be set during the configuration process prior to installing Philologic3.