Been years since I used Traktor, so bit rusty on the settings.
1) Pick the right audio device (driver) on the Audio Setup tab under “Audio Device” (duh!). This should probably be the Denon DJ ASIO Driver if I recall correctly (at least it was with my MC6000 I think).
2) On the Output Routing tab, select “External” for Mixing Mode (as you have).
3) Now set Output Deck A to (for example) channel 1 L and channel 1 R or Front L and Front R. You should have 4 options (or even more if you use a higher channel count sound card, but generally it will be 4 for a controller like the MC6000)
4) Set Output Deck B to something different! It could be marked as channel 2 L + R or Back L + R.
If you have only 1 set (of stereo, thus L + R) of options, like you describe with front left/front right, something is wrong. Either the wrong device selected or the wrong device driver (not) installed. Probably the right driver can be found at the Denon site. You can also try the ASIO4All drivers from their site.
But you should have the option to choose from 4 (2 x a L+R combo), otherwise it won’t work properly.