AnalysisSkeleton have three jobOptions files, e.g.,

_topOptions.py
_topOptions_AutoConfig.py
_topOptions_New.py

Please look at https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PhysicsAnalysisWorkBookAODAnalysisRel15#What_s_NEW_on_this_page for an explanation

Also see https://twiki.cern.ch/twiki/bin/view/AtlasProtected/PhysicsAnalysisWorkBookFullAODAnalysisRel15 to learn how the file with _NEW suffix is used.
