@Tony You will eventually get a gut feeling for where certain files "should" be. User configuration for system wide programs, those are usually in /etc/<program>/<somefile with a particular name>.{conf,yaml,toml,json,etc}
Internal program data usually lives in /var/lib/<program>
Software I build and install I usually put in /opt
etc etc etc. The directory sprawl is sort of cultural and will get less weird the more you interact with it.