Import external modules yaml config through own hook_update_N implementation
If you have no data then reinstall the module.

If you want to keep the data then this depends what you have changed in the configuration. You can try how far you can get with the method you've described. If you only add fields, this will probably work. Also minor changes to a field can work. But if you change how a field is stored in the database this will not work.

The official way to do this is described here https://www.drupal.org/node/2554097.