There is two external decayers available in FairRoot:
In the simulation macro you need to call:
fRun->SetPythiadecayer(kTRUE)
And then in the DecayConfig.C you specify for which particles Pythia should be used as decayeer. See the comments in the DecayConfig.C file.
fRun->SetUserDecay(kTRUE)
And then in the UserDecay.C macro you specify for which particles this decayer has to be used and the two/three particle phase space decay mode and branching ratios. (see the UserDecay.C file for an example)