The CO needs setting accordingly to what the chip author has specified, however you need a exhaust gas analyzer to do so, something which most don't have.
When you fitted the actuator did you pre load it first?
The trouble is fitting the stuff is easy enough to do you need to get the fuelling checked out after to make sure it's running ok despite it being an 'off the shelf chip'.
You are kind of right the ECU will manage the engine's fuelling requirements etc, however it can only do as it has been told hence why you need to change the 'Mapping' when you make a change to the engine so it is calibrated for that spec.
I guess it feels flat as it's probably not making any boost.
How do you know it was overboosting?
Martin