The only thing a pc will do is look at the amount (%) the throttle is opened at whatever rpm the engine is doing and add or subtract a percentage of fuel onto whatever the original map is supplying.
The pc map is just a table with % throttle across the top end engine rpm every 250 down the side, where the two cross (throttle/rpm) that is the % it will alter it, if the bike is on the over-run and not fuelling at all the pc can not add or subtract anything as there is nothing there to start with.
If you leave the O2/lambda's in circuit the pc and original ecu will fight each other.
The pc is a very easy user friendly device, that is why they are so popular