Hi Almc and welcome to TorqueCars nice to hav eyou along. The A'pexi AFC NEO is a fuel management computer which piggybacks on to your ECU. The standard ECU paramters will as far as I know be overwritten via the piggy back which will effectively take over the fuelling.
I don't think you will see much of a power gain overall though, you would surely be better off going for the full Apexi engine management unit which replaces the ECU altogether. Have you done any other mods? You should think about induction kit, sports exhaust and cams if you are serious about power and they will help you get the max from your A'pexi AFC NEO