frank,
You are talking about ECU tuning for the ignition timing map?
Yes, you tune your piggyback with WI, you need WI for optimum and safe operation.
However, to use the WI effectively, we need a piggyback that can switch map, from map 1, which is standard timning, to map 2, which is advanced timing.
The switching can be activated together with the WI activation.
For such application, it's recomended to use the stage II kit with MAF/MAP referrence, which allows a variable spray volume according to engine load, since ignition timing is also controlled by the engine load. HOwever, do not misunderstand that the Boost Cooler controller is meant to tuneyour ECU (as a piggyback), it's just a controller for the WI system.
Anyway, I am not using any such piggyback as I have not found one that suits the application.
For force induction, tuner can use an electronic boost controller to controller the turbine boost, simultaneously with the stage II WI system.