I use Drupal VM with php5-fpm and it uses port 9000 so I just set my debug ports to 9001.
- Set the debug port to 9001 in PHPStorm
- Create a new server in PHPStorm:
- Preferences >> Languages & Framworks >> Servers
- Add a Name: and Host: e.g., mysite.dev (for both)
- Click the checkbox: Use path mappings...
- I always map my local DRUPAL_ROOT to my VM DRUPAL_ROOT