I'm right there with you so I created a single config file in frontend/config and created a symlink in every module's config folder linking to the frontend file.
Create this as your master config:
/path/to/project/root/apps/frontend/config/config.php
the create a symlink for backend:
ln -s /path/to/project/root/apps/frontend/config/config.php /path/to/project/root/apps/backend/config/config.php