I am wondering if one could run two blogs http://www.anotherdomain.com/de/ and http://www.anotherdomain.com/en/ in a system with so far having http://sub1.anotherdomain.com/ running via http://www.maindomain.com/ WITHOUT now also directing http://anotherdomain.com itself to http://www.maindomain.com/

We wanted avoid loosing subdirectories in anotherdomain.com, which can not be addressed as http://anotherdomain.com/media or http://anotherdomain.com/docs anymore once the domains is directed to http://www.maindomain.com/

Or do we have something else messed up to not get what we wanted?