We　study　the　dynamics　of　a　coupled　cavity　system　composed　of　three　cavities,　and　propose　a　scheme　for　the　coherent　manipulation　of　two　collective　atomic　modes　by　a　control　atom.　In　the　scheme,　the　control　atom　and　two　atomic　ensembles　interact　with　the　local　cavity　mode,　while　the　control　atom　is　externally　driven　by　a　laser　field.　We　show　that　under　certain　conditions,　the　dynamics　of　the　whole　system　are　reduced　to　an　effective　coherent　coupling　between　the　control　atom　and　two　collective　atomic　modes,　while　the　cavity　fields　are　only　virtually　excited.　We　also　study　the　dynamics　of　the　entanglement　generation　of　the　two　distant　collective　atomic　modes.　The　scheme　provides　a　potential　application　for　quantum-state　engineering　and　quantum　control.