Welcome to the more than 4 channel recorder club. Check your firmware version and update it if its not one the most recent or 2nd most recent. You can download firmware update and the complete user manual as a PDF on the DR-680 page of the Tascam website.
The mix file is always 2-ch stereo and can be turned on or off, or alternately set to record the SPDIF input seperately from the other channels (but still synced) which providings the capability of recoding 8 seperate channels.
Sometimes I set the machine to write mono files if those don't consist of obvious stereo pairs or if I want to double the recording time before a file split occurs. Other times I set it to make multiple 2 channel files because that has the advantage of easy direct stereo playback from the computer without doing anything to the files.