So you checked the box and clicked OK? Great so now you have the Content Organizer Feature and the correspondent Drop Off Library enabled on every single site of every site collection of every Web Application in that farm. If this is your goal, great! If not keep reading to find out how to contain this small disaster whithout the need of going to every site and do things manually.
Actually Chris Kent wrote a briliant blog post exactly on how to solve this mess, check it out and good luck.
Thank you Chris.