It depends what file format and codec you are exporting to. Some file types support exporting multitrack, and others do not.
Also, are you running your multichannel audio file through Premiere Pro and Queing the video through Media Encoder that way? If you're wanting more than just a stereo track, then you'll have to make sure that your Premiere Pro sequence setting for master audio track is set to "Multichannel," not "Stereo." If you find that your sequence settings are set to stereo, you can create a new sequence with the same exact video settings, but set the audio master to "Multichannel." Then just copy everything in your original sequence onto that new one, and you'll have the option for channel routing and multichannel exporting.