Yes graggy, each unit can use its own transducer even though they are Ethernet connected. However, there is the possibility of sonar-to-sonar interference (sonar cross-talk) for the 2D 200kHz sonar and the Si sonar (but only if you have the trolling motor mounted HDSi transducer turned 90 degrees such that either the left or right Si beam is pointing at the rear HDSi transducer). For the 2D sonar interference you can try turning on and up the Noise Filter menu.
Setting each unit to use its own transducer is not needed, they should do this by default. Do you have a copy of the Ethernet manual?