these are the location of the dark aeons:-

dark valefor=besaid village
dark ifrit=sanubia desert.
dark ixion=thunder plains north near save sphere
dark shiva=macalania temple,entrance
dark bahamut=zanarkand dome,the beyond.
dark yojimbo=cavern of the stolen fayth,near save sphere.
dark anima=gagazet,mountain gate.

dark sindy=(magus sister 1)
dark sandy =(magus sister 2)
dark mindy=(magus sister 3) they can all be found on the mushroom rock road.location unknown

the dark aeons will appear once u have completed all the tasks relevant to the story...

hope this helps.....