the second one in the upper horn controls the piezo acoustic pickup. You can turn it on, mix it with the magnetic pickups or turn on just the magnetics.
The 3-way switch closest to the volume knob switches the magnetic pickups.
(bridge humbucker, inner coil of each humbucker, neck humbucker)
If the guitar has the piezo option, the other toggle (on the guitar's upper horn) selects magnetic pickup output only, piezo output only, or both outputs simultaneously.
Depends on the other options--matching or natural headstock, JP or plain inlays, upcharge color (especially Mystic Dream +$400 retail)--but a fully loaded JP in a "standard" color runs around $1700 or so. A Mystic Dream is closer to $2000 and a plain headstock/dot inlays/standard color is maybe $1600 or so.