Any component in the App_Code folder is compiled in the same way as an ASP.NET page.
App_Code folder are compiled into a new assembly and saved to the Temporary ASP .NET Files folder, located at the following path:
C:\WINDOWS\Microsoft.NET\Framework\v2.0.50727\Temporary ASP.NET Files\[application name]
You can add as many subfolders to the App_Code folder as you need to organize your components.