When you have an airship, talk to Cid, and choose the second option in Map menu (Search). The secret place are:

Secret Place #1 X: 34 Y: 58
Secret Place #2 X: 15 Y: 41
Secret Place #3 X: 31 Y: 73
Secret Place #4 X: 16 Y: 57
Secret Place #5 X: 42 Y: 57
Secret Place #6 X: 74 Y: 36