This may help explain things better, Stock fuel map from pulsar, with approx fuel ratios used in each cell:
The light blue cells are closed loop area. The ecu uses the feedback from the O2 sensor to maintain economy here. If you try and alter this part of the map with an external fuel controller, be that a SAFC etc, and you leave the O2 sensor connected the ECU will remove what ever changes you make and be working against you. You wouldn't want to do this anyway.
Now one thing you need to know the RPM is obviously on the left hand scale. The top scale is load, it basically represents airflow. A stock pulsar at 1.2 bar will go off the end of the load axis, and also the airflow meter and injectors will all be on their limits (or VERY close). This is the case even with a Mines ECU (the injectors and afm anyway) I have not yet downloaded a map from a mines ECU, so I don't know if the load axis is rescaled or not. (Its only a matter of time before I get my hands on one however). Its not an ideal position to be in, but reality is it may be ok, its when you go beyond this that you'll begin to get fuel leaning out, as the injectors are already maxed out etc..
When you use a piggy back ecu to change injectors sizes (except e-manage ultimate) they do so by altering the airflow voltage. Now this is all very well, and it can work well, however you can see if it alters it too much, you may not get far enough across the load map to get the right AFRs for the particular engine load. This is when you will need to make corrections. This is even more so important when you consider the ignition map. When the turbo begins to generate boost you pull a significant amount of timing out. If you alter the load points then this can change, if your not aware what is going on or how to check this you may find you run too much ignition advance and combined with altered fuel and other contributing factors you may even experience knock.
Anyway, hopefully this will be of some interest to you.
Ed