Ok I achieved this through using Mapped Instrument in the Environment window. I mapped 32 keys worth on 3 banks 8/16 (main)/8 ... That was the whole set to Drumkit Designer. Page 38+ of the Quneo Full Manual it give you the details of which MIDI codes to use for the lights. I referenced this and set my kicks and snares to output red on the desired pad. Everything else is green. I have the high hat as a red-green top-left dot.
Say the Kick is C1 but the pad is Pad 1.. set the output note to C-2 (green) or C#-2 (red) in the Mapped Instrument of the Environment window. I created a new layer just for this. There you set the Port to QUNEO. I set it on Channel 1 since that will base the [BASE] channel. You can change the base to channel 2 or 3 for the different light associations.
After you configure Mapped Instrument then, find the drum track or whatever you're working with in the Environment window. Have the layer you created and open a new environment. when you find the drum track drag the cable from that track to the Mapped Instrument in the other environment window.
Now you can record your drums and when you play them back they will feedback on the leds you associated them with.
Very simple procedure. I'll make a youtube tutorial about how I did this very soon. I just wanted to accomplish this for once and share.
P.S. Another way is to use preset midi regions with LED effects you can make here: http://projects.keithmcmillen.com/quneopadanimator/
In the environment instead of Mapped Instrument use Touch Tracks. Drag the region onto the key you want to trigger it with. Connect the cable as above and voila!