Are you wanting this sound for live applications, recording or both? I can share with you what I use for both.
For live: Martin HD28V with a fishman under-saddle pickup and the Fishman Pro Platinum EQ DI box. Sometimes I go into the PA with it or through an Acoustic Amp. That's an active pickup. I've used other Acoustic guitars without an active pickup into the Fishman Pro Plat. E.Q. which will boost your signal before your main amp. It has a notch filter on it so you can tune out that unwanted feedback if you are running your input to an amp with 2x12 speakers.
For recording: I use a large condensor Mic pointed at about the 12th fret away from the guitar. You just have to move your Mic to find the sweet spot. I run that signal through a Focusrite VoiceMaster Plat. Pro. into any recording device.
So to kind of answer your question, I really never use my Gnx3 for an Acoustic guitar. I do agree the "acoustic guitar" patch is really not that good.
However, the Gnx3 will boost your signal, it is a preamp in a sense. If you are hell bent on using the Gnx3 with your passive pickup try these setting:
AMP = Direct, Blackface, or CleanTube
Cabinet: Direct, or 65 1x12
Amp Parameters= don't adjust the Gain too high. no more then 50
Noise Gate= On
EQ= your choice
Compressor=Off
Hope that helps.