Gui got it right. By disabling the bypass actuator no boost will be applied to the engine so it will run like normal. Once a tune is setup you'll be able to run boosted. A key item is to have a functional 2 Bar MAP sensor so the engine can sense the pressure, this will have to be changed AFTER you get it to the tuner as it will read improperly for a normal tune.
Might have been wise to start with the full GM kit as it included injectors, sensors and access to a GM tune (which isn't great but does work). I went this route and even without using the HPTuner yet the results have been very good.
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