The PC3 Powercommander is a piggy back system... What it does is "fools" the factory settings in the Delphi ECU... It does not overwrite the stock factory settings in the ECU... Once you unplugg the PC3, the motor reverts back to the stock factory settings in the Delphi ECU...
Whatever settings are on the stock Delphi ECU will remain... The only way you can change the settings is to have one of the HD tuners or a scanalyzer... With a scanalyser, the tech can do a "flash" to the ECU, stage I, stage II ect... Basically, what this does is changes the AFR settings in the ECU, rev limit changes etc...
If your bike is running good and you add in the PC3 piggy back tuner, you will have to find a map that closely resembles your motor and what mods were done, exhaust, airfilter, etc... Then you load the map into the PC3, from there you can make adjustments to the AFR with three external buttons that control how much fuel is getting to the injectors... The buttons regulate low, mid, high meaning, the low button adjust fuel from idle to 25% TPS, mid controls from 25% to 75% TPS and high controls fuel from 75% to 100% TPS... You can add more fuel or remove more fuel by pushing the buttons on the PC3...
Hope this helps...