When it comes to the right location for the configuration file, you are basically free to choose one. You have three possibilities:
Per default, Annotate will look at /usr/local/etc/annotate.conf.
If you have access to the environment of your CGI scripts, you can set the environment variable ANNOTATE_CONF to point to the configuration file. This can be done with Apache's SetEnv directive:
SetEnv ANNOTATE_CONF "/path/to/annotate.conf"
The third alternative is to set the path directly in ConfigFile.pm. If neither of the above methods work for you, this is the way to go.
Don't
put the configuration file to a location that is readable from the
outside. The configuration file will include details about your setup
(i.e. a password to the database) which you most probably don't want
to disclose. So be careful.Warning