Let's get practical.
First listen for incoming debugging sessions.
Just double click the methods name so it is fully selected. Then make a right click and select your external tool to run a single file or method.
The currently opened file will be passed as well as the method you've selected.
Simply open the file, make a right click and select your external tool to run a single file or method. The currently opened file will be passed via PHPStorm variable to the run command.
Simply open the file navigator and right click on the directory you want. The select your external tool to run a single file or method.
The directory will be passed via --file= and all tests within this directory will be executed.
Click right anywhere in your code or open the "Tools" menu from the main menu and select your external tool to run all files/tests.