It is not recommended to update directly Sitecore files because you will have problems on updating Sitecore and is really difficult to know what exactly you changed.
Since Sitecore runs within IIS, it is natural for Sitecore to be configured using IIS’s configuration file, Web.config.
The path to Sitecore-specific settings is /configuration/sitecore.
Sitecore supports distributed configuration. This means that Sitecore-specific settings (those settings located under /configuration/sitecore) can be spread out between multiple files. The process Sitecore uses to merge multiple config files is called called “config patching”.
How Patching Works
Sitecore uses a custom configuration section handler to merge patch files. The handler finds files with the .config extension in the /App_Config/Include folder and combines the files it finds with Web.config. The combined configuration is used at runtime.
Patch File Names
Patch files are merged with Web.config in alphabetical order. This means configuration in a patch file named a.config will appear before configuration in a patch file named b.config.
When the same configuration is found in multiple patch files, the configuration from the last patch file processed is the configuration that is used.
Patch File Folders
Subfolders of /App_Config/Include are processed after files in the /App_Config/Includefolder. Folders are processed in alphabetical order, as are the files in each folder.
For example, if the same configuration is defined in the following files the configuration from the last file listed is used:
Patching only works on the Sitecore configuration section. This is located in Web.config under /configuration/sitecore. Configuration in other sections of Web.config cannot be controlled through patching.
How to See the Result of Patching
Since the Sitecore configuration is the result of the merging of configuration from Web.config with a variable number of patch files, you cannot look at Web.config or any individual patch file in order to determine the configuration Sitecore is using. Sitecore includes an admin script to do this.
The script displays the results of the config file patching process.
More information can be found here:
Starting from Sitecore 9 we have OOTB configuration layers.
Using Configuration Layers/Roles You don't need a patch for your patch on different roles (CM,CD, Proc, Rep, etc) Just deploy everything and set the server role.
Sitecore divides configuration files into layers. Each layer consists of a dedicated folder under the App_config folder. By default, there are four layers:
Each layer influences a specific area of Sitecore functionality.
Sitecore divides the configuration files into layers in order to:
Give you better control over when Sitecore loads files at runtime.
Allow you to disable all configuration files in a layer at once.
More informations can be found here: https://doc.sitecore.com/developers/90/platform-administration-and-architecture/en/configuration-layers.html
If your Sitecore solution is 8.1 Update 3 or Sitecore 8.2 you can install a Sitecore Configuration Roles module .https://github.com/Sitecore/Sitecore-Configuration-Roles