Lots of software looks at several places for configfiles. Ie. a systemwide config and a user-specific config. Usually the user-specific config can override the systemwide config (exception is security-type options for instance). User-specific configs usually live in a users home directory (on UNIX as .<appname>rc files, like .cvsrc ).
My advice would be to consider using a 2 configfile type of approach, make it work in all three situations ( system-config + user-config, system-config + no user-config, no system-config + user-config ) and document what overrides what.