By default htop reads its configuration from the XDG-compliant path ~/.config/htop/htoprc -- the configuration file is overwritten by htop's in-program Setup configuration, so it should not be hand-edited. If no user configuration exists htop tries to read the system- wide configuration from /etc/htoprc and as a last resort, falls back to its hard coded defaults.
You may override the location of the configuration file using the $HTOPRC environment variable (so you can have multiple configurations for different machines that share the same home directory, for example).