Hi Ben,
As a full-duplex RS-485 interface, the state machine <----> module connection has polarity. In other words, the wiring on one side (A) has to be the opposite of the wiring on the other side (B). The module jacks on the state machine are all 'A', and the "state machine" jack on all modules + the Arduino shield are 'B'. For Module <----> Module connections, we adopted the convention that modules that capture signals (e.g. Analog input, Rotary encoder) are 'B', and modules that generate signals (e.g. Analog output, DDS) are 'A'. This creates a problem for your application - the Arduino shield is type 'B', but so is the 'Module' jack on the rotary encoder module (I'm going by the thread title here). If you have a DDS module, you can connect its 'Input Stream' jack to an Arduino shield (not sure if this is what you meant).
-Josh
