Hi
I am actually having a similar problem to yours but I think I can help....
1st load Kontakt with all stereo outputs selected
2nd in the output section of Kontakt > Presets Batch Configutation > Batch Functions > Clear output section and create one individual channel for each intrument loaded.
That will now give you an individual output for each instrument in sonar, the input to each associated audio track in sonar will tell you where it is patched to in Kontakt so you can relabel each track.
Hope that helps?
The problem for me is I am using Steven Slate Drums which has two auxilary outputs which in SSD are Room Mics (NRG room and SSD Room). Kontakt only gives you 4 routing options in Kontakt for these Aux outputs which are to the same outputs as the first 4 instruments ie Kick drum on outputs 1&2, Auxilary outs also to outputs 1&2 which have the kick drum on them, so room mics and kick appear on the same audio track in X1. I cant see a way round this. This was never a problem in Kontakt 3.5 or 4.
Anyhow I hope the first part helps with your issue.