Yes, you can configure which config file you want to use. Look at this part of the doc.
http://docs.behat.org/guides/7.config.html#paths
What error do you get when running your command?
php bin/behat --config app/config/behat.yml
This error?
[RuntimeException]
Context class not found.
Maybe you have provided a wrong or no `bootstrap` path in your behat.yml:
http://docs.behat.org/guides/7.config.html#paths
If that's the case, I think if might be because you need to specify where to find the features in your behat.yml file.
Now you moved the file to /app/config/behat.yml, the related path from behat.yml to the feature directory has changed, so you should add the following to the file:
default:
paths:
features: ../features/
bootstrap: ../features/bootstrap