Take some time to try the guitar presets. I remember the Baggs M1 magnetic soundhole pickup wasn't too far off running flat. If your pickup is magnetic, this might be ok. Also, turn the knobs of the remote, flavor to your taste. Try all the acoustic guitar ones too.
Have someone play the guitar with the system off and listen to it. Then turn the system up and shoot for the same sound. I'll bet there's a preset that works for you.
