As you may know we don't support QoS on aggregate interface.
Which mode are you running the PA in? VWire? Routing L3 mode? If L3 modeis not a requirement, you can put our box as VWire intercepting all those physical connections created for aggregate interface. All the outside facing interfaces should be in the same zone,say untrust; and all the inside facing interfaces should be in the same zone too, say trust. Then PA will do content ID, APP Id and User ID based on the two zones- you don't need aggregate interfaces setup in PA, we just use multiple VWire to intercept all the physical connections and analyze the traffic at zone level.
Apply QoS on all egress interfaces.
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