This paper considers process-aware modifications to real-time code running on embedded devices in cyber-physical systems (CPS) so as to create signatures in analog side channel signals without impacting process characteristics. We consider side channel signals emanating from the digital components of the CPS as well as from physical instrumentation such as actuators. We show that code in an embedded device can be instrumented to shape the side channel signals so as to carry auxiliary information without appreciably altering the stability and performance characteristics of the closed-loop process. Inserting auxiliary information into analog side channels can be used both for attack (e.g., leaking information) and defense (e.g., remote real-time monitoring) purposes. The proposed process-aware side channel shaping approach is demonstrated on the Tennessee Eastman process control benchmark implemented in a hardware-in-the-loop simulator.