Hey Justin, by CDI, you mean a "capacitive discharge ignition"? If so, its not needed, the ignition is very powerful in the Stage II, it will easily fire 45k volts through the coil, no external CDI or any other hardware needed.
Other than that, the Stage II unit has 8 igniton channels, so for a 16v you could set up 8 coils, one to fire every other comb. event, keep your coils nice and cool
Hope that answers your question, if not gimme some more details.
Sure, its a capacitive discharge, you could use it if you wanted too, but definitely not required, I'd recommend not using it.
We have a test fixture set up with 8 huge MSD coils and some beefy MSD spark plugs, heavy spark plug wire, coil wires, etc. We've run a Stage IIc ECU up to 30k rpm on this test fixture (over 40k rpm with a 4 cylinder config), the spark plugs creating a brilliant arch cleanly firing all the way up. The sound is amazing, and surprisingly loud, you literally have to plug your ears. The ECU continues to operate happily for a few minutes like this, soon the spark plugs begin to heat up and glow, so badly that they begin to meld and fail - they don't last too long like this, but the ECU is hardly breaking a sweat, not even drawing more than 40A during the whole process. 8)