Recently, I’ve been changing the organization method I’m using when architecting builds for my clients. Sitecore supports automatically patching in include files from subfolders of App_Config\Include, which allows for architecting project-specific overrides and environment-specific settings in a much cleaner manner.

Kamruz Jaman just wrote a great post about this on Friday. The upshot? Stop putting your files in the primary Include folder and make sure you use subfolders!

Another few tips to add to the post:

1. Use a naming convention for environment files. You want to make sure you have a way for deployment scripts to determine whether a file belongs to your primary or secondary content delivery server, or if it applies to all environments. An example would be PRD.CD1.CustomSettings.config.example for a file you want to deploy to your primary production environment.
2. Use .example for files intended for other environments. If you are trying to manage all of your environment-specific files in a single solution, you will need .example extensions on the files. Otherwise, these files will all activate in your local development.