EMC compliance must be achieved for the final product with typical application wiring (power supply, signal and communication cables). I don't understand what you mean by "have to define dB levels for both"?. Conducted emissions are measured at the external power supply lines, possibly also other external cables.
Question is which modules are expected to act as dominant interference sources and which are probably filtering and transmitting the interferences. In case of doubt, a switch mode PSU is able to generate noise over the full conducted 0.15 - 30 MHz range.