I am running a GSXR600 with EMU Black V3 and as already mentioned you need to run the secondary injectors in batch injection mode. This means that fuel is injected at the same time for all secondary injectors twice per engine cycle. The EMU black does not support sequential injection for the secondary stage. In my opinion batch injection works fine for the secondary stage since the secondary stage anyway only is active at high RPM and high throttle openings.
I had some issues with the secondary injection which were resolved in this thread
This is my configuration
