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 in httpd.conf (or similar
configuration files):
The third possibility is to set the path directly in
AnnotateConfig.pm. If neither of the above
methods work for you, this is the way to go.