The fuel map is stored in the PCIII and it intercepts and changes the signal from the ECU to the fuel injectors. There is no change to the map loaded into the ECU.
So you load a "full power" map into the ECU via Tuneboy, load a zero map into the PCIII, then dyno tune the bike on a dynojet dyno via PCIII, then remove the PCIII, download the PCIII map to your computer, then import the PCIII map into the Tuneboy map you had loaded into the ECU, then load that tune into the ECU. Then there is no need for the PCIII on the bike. And you got a dyno tune that took 1 hour instead of 8+ hours.