@rorak > Don't worry about the input channel numbers, unfortunately that's just the way they appear. ;) It should still work out to be the same if you connect them as 0 - 1, and 2 - 3, then 4 - 5, lastly 6 - 7.
I'm not exactly sure what you mean by " the audio went through the mixer but no time code control"?
Did you have a timecode CD in a CDJ connected to the mixer?
Yes, if you watch Pulse's video HERE, at 3:00 you can see the timecode signal in the "Preferences" window under "Timecode Setup".
If you could please follow that video I posted above, and please also take a look at this video HERE.
As for the MIDI settings... the DJM-900 is not meant to control the Traktor software. It is to be used as a hardware mixer that is Traktor certified and can replace the Audio XX DJ sound card from NI. ;)
I hope those videos are helpful and please feel free to ask more questions if need. :)