[jgg]

You've got about four different questions rolled up into one. I'll try to break things out for you. The short answer is that the output setting is asking how many USB channels to assign to bring audio from the virus into your computer. Unless you're using a second multi-channel sound card and are doing projects like I describe below, or recording more than one voice at a time, Stereo is just fine.

As to the multiple Viruses, this only makes sense if you actually have more than one Virus device. If you do (lucky you), first try the stand alone software "Virus Control Center". This should see both devices, allow you to give them unique names, and hopefully they will show up as separate devices in your DAW.

The Virus has 3 play modes; single, multi and sequencer. When you have your Virus connected to your computer and the Virus Control Software launched, the Virus goes into sequencer mode. Sequencer mode allows you to load 16 different patches simultaneously but you can't save the set. Outside of the Virus Control software, "Multi Mode" also allows 16 channels of patches but you can save them - up to 128 sets to bring back instantly later. You can modify each channel to respond to different midi channels - which allows you to layer multiple patches together at once (i.e. one note plays 2 or more sounds together). "Single Mode" is where you usually are when the computer's disconnected and you are working on a patch.

For each channel(!) you have a choice of one of six stereo outputs or twelve mono outputs, plus a choice of a surround pair. You can set the balance and surround pan, and also use both as a modulation targets to move sounds around the four channels. Three of the stereo pairs are on the back of the unit (the first pair is the same as headphone out and the digital out - if you want consistency across all the channels use just the analog outs). The other three are via USB back to the computer - to use these you need a multi-channel sound card. I use a Presonus Firestudio 2626 myself. Remember - the choice of outputs is PER CHANNEL - you've got 16! That means you can have 16 different voices each panning complexly each across a different subset of four channels across a total of twelve output channels, possibly all triggered by one note. Find yourself two six plus channel amplifiers and twelve speakers, you'll never go back. You can make Jupiter 8's sound like a toy piano.

The output mode you want for this is "multi output", and you'll have to figure out how to configure the routing in your DAW software. It's pretty easy to set up a six channel version with just the analog outputs to see what it's like.

The input settings depend on if you want to use the Virus outputs as your computer's sound card, or are doing side chain effects (routing computer tracks through the Virus's effects). If you use the Virus analog inputs, you have to give up one of the USB channels.

75% of the time I've got the Virus in single mode, loading patches, tweaking knobs, and I'm wearing headphones. 15% of the time I'm playing on a master keyboard where I can select which channels are active, the Virus is in multi mode, I'm playing with layers, and I'm still wearing headphones. The last 10% the girlfriend's away, the house is shaking, and the cat's under the bed.

Hope this helps.
JGG