3 phase rocks...I use a rotary phase converter for my machine tools. Took me a while to figger out, but it has MANY benefits over household electricity.
The only difference between this and a single phase 240v build is that you are using 3 phase SSR's and breakers. Size your wires and breakers according to amperage (of course).The PID output signal should be no different...but you need to route it differently. IMHO, you should get a rotary switch that controls the ssr CONTROL signal from the PID....that way the PID would switch either one, two, three, or none of the SSR's. Use contactors to control the actual power-handling circuits.