BepInEx 6 contains all configuration files in BepInEx/config folder.
All configuration files have .cfg extension and follow TOML-like syntax.

Configuring BepInEx

The main BepInEx configuration is located in BepInEx/config/BepInEx.cfg.
If you don't have the file, run the game with BepInEx at least once, and BepInEx automatically generates the file.

Open the file in any text editor of your choice. All configuration options are documented.

Configuring plugins

Most plugins have their configuration options in BepInEx/config folder.
The configuration files are named by the GUID of the plugin.
Options are usually documented, but that depends on the plugin developer.

It is suggested to download and use BepInEx.ConfigurationManager which provides a simple, in-game UI for editing the plugin configuration.