user.js is the supported and reliable way to set preferences that should just be set no matter what the default configuration is or what about:config says. pre

user.js is the supported and reliable way to set preferences that should just be set no matter what the default configuration is or what about:config says. prefs.js is the storage for the current non-default pref values. At runtime, default pref values are loaded, then prefs.js, then user.js. You _can_ edit prefs.js and the effect will be the same as if you changed the pref in about:config, as long as you do it while Firefox is not running against that profile. If you do it while Firefox is running, your changes will be overwritten at shutdown when Firefox writes out then-current in-memory pref values.