Sorry for not getting back, I've been playing with some new software...
Right. To configure as a synth you go the Utilities Menu > Plug-in Manager > VST Audio Effects and find the Pod Farm plug-in. Click on it and press the Plug-in Properties button below.
There's a box that you tick - "Configure as a synth". Hit OK.
Now you have to remember to go the the Soft Synths menu when adding PF, not the Audio FX. When configured this way you can use an expression pedal to control the wahs and turn the effects on and off using the controls on a midi keyboard etc.
As for the knob 1 and knob 16 thing - I'd suggest creating a fresh patch, add a wah and then see what happens in Sonar as it should work fine (as nothing would have been assigned to any of the knobs).
Grum.