Polyphonic processing in Audulus works seamlessly. A connection between nodes is polyphonic if it is rendered thicker. Nodes are automatically capable of polyphonic processing. So for example, feed a Distortion node with a polyphonic connection and the distortion will be applied separately to each voice in the connection.
A good example of polyphonic processing is the Subtractive example. Set the Keyboard node to "poly" and note the thicker polyphonic connections. That is, up until the voices are mixed down by the PolyToMono node.