The inputs will be mono.

Best solution would be to ditch the mixer (which is probably adding noise anyway) and just grab a multi input audio interface like a Saffire Pro 40. This will give you enough inputs to configure some as stereo pairs, or even mono signals. You will be able to route the interfaces outputs within your DAW in any configuration you want.

___________________
Soundcloud

Are you referring to the Audio Kontrol 1, or the Audio Kontrol 6? If it's the K1, then yeah, I totally agree with tehlord - don't waste your time, just ditch the mixer and get an interface with 2 stereo line level inputs. If it's the K6, then, yes, you can do what you're hoping to do by running one synth into the stereo 1/4-in TRS and the other into the two mono mic/instrument inputs on the front panel. But, that's not really the most elegant way to go because you'd see one synth come into a stereo track in your DAW, but the other would come in as two mono tracks that you'd have to pan L/R (unless the NI driver allows you to sum the 2 front panel mono inputs into one stereo).

___________________
cryophonik.com | facebook | soundcloud

Sonar Platinum | Ableton Live 9 | Logic Pro X | Access Virus TI2 Keyboard | Kurzweil PC3X | Nord Lead 4R | NI Maschine

I'm pretty sure he's refering to the audio kontrol 1... i don't think someone would be giving away the 6 one.. besides it's called the komplete audio 6 (confusing name yes... i don't know why NI would call it that)

Yep its the audio kontrol 1. Thanks for your help guys. Audio interface it is.

___________________
SOUNDCLOUD UPDATED
http://soundcloud.com/narel-1
Latest releases:
Audio Noir 'Revelation' (Narel Remix) (Bonzai & Perfecto)
06R 'Air 2.0' (Narel's Warm Air Remix) (Green Martian)
Narel 'The Machines Were Dreaming' (L*C*D Recordings)