I have never used my JPs in multimode but I guess there's not a real multimode available. You have to use the performance mode and then you have 2 layers in use. I guess you have to choose from the layer's setting which output and midi channel it uses. By default they use the same midi channel and output to stereo.
In preformance mode you can select the upper and lower layers or both by pressing the button (I don't remember the name). So you can edit the 2 layers separately when you select either lower or upper layer. Remember that if you have both layers selected and tweak something it affects both layers and you might loose some important settings of the other layer! If you want to make those super fat supersaw sounds, use the dual layer mode for all the filter + envelope + effects tweaking but tweak both layer's supersaw detune separately by selecting upper or lower layer.
I usually don't like multimodes and use only 1 sound per synth at a time.
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