Hi, I have a guitar equiped with Fishman piezo, it’s output providing 2 signals I can plug in my audio interface.
Unfortunately we can’t stake the amps and select one input for piezo amp and the other for other amps 
I know, it can be done in a daw, but it should have been so nice to not start daw just for this.
Wouldn’t that be the same for all plugins if not using a DAW? The DAW allows you to have multiple inputs and routing etc.
I think you can run stereo into the plugins, but you can’t split the signal chains into separate “scenes” to run different amps. So I see what OP is saying, being able to take line A and run one preset, and line B and run another, either in parallel or one at a time.
For the Archetype Petrucci, it almost seems like a given that it should work with 2 signals, considering that this is the way that John uses his rig.
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Would be a great feature, but they’d have to redesign it from the ground up; where do the signals mix? Would you have two entirely separate chains for each signal? I think the best bet for that one right now is using two instances in a DAW and scultping the signal for each as you see fit.