The most important thing to note here is that the XDJ-1000s will not be producing sound–they're acting only as MIDI controllers. If you're using a MacBook Pro, purchase a quality AC powered USB hub and connect your XDJs to it. Connect your mixer directly to your MacBook Pro via USB.
1. Make sure your version of Traktor is up-to-date (or a recent version that natively supports XDJ-1000 HID, 2.8 was the earliest I believe).
2. Ensure your DJM and XDJ have been updated with most recent firmware. Ensure your XDJ preferences for MIDI/HID is set to Advance.
3. In Traktor, go to Preferences>Controller Manager and select XDJ-1000 under Device tab.
4. On the XDJ-1000, press the "Link" button. Then press the rotary knob to select "USB MIDI." Select a deck for the XDJ to represent (A,B,C or D). I'd recommend having one as A and the other as B to keep things simple.
5. Now we have your units connected, but we need sound. Go to Traktor Preferences>Audio Setup. Select the DJM-900 as your audio interface.
6. The important part: routing. Go to Preferences>Output Routing. Be sure mixing mode is set to External.
7. On the Pioneer Mixer, adjust the Channel Switches for Channel 2 and Channel 3 to USB. Note the respective numbers (3/4 for Channel 2, 5/6 for Channel 3).
8. In Traktor's Preferences>Output Routing, change Output Deck A routing to DJM900nexus 3 and DJM900nexus 4. Change Output Deck B routing to DJM900nexus 5 and DJM900nexus 6.
You should be all set. If this doesn't work, create screen grabs of your preference settings or create a video so we can better understand your setup.
Cheers.