you can just create what ever directory structure you like in your src folder and move your php files to those sub directories. After doing that, just run dev/build?flush=all in your browser to make SilverStripe to rescan your php files.
That should do it :).
You can also namespace your php classes so that they contain the sub folder names that you just created, but SilverStripe doesn’t require this. It’s just a cleaner way to do namespacing especially in bigger projects. It just helps you to find the class file location if you see the class name + namespace referenced in another location.