Start out by playing your game in the Chocobo's Forest.
Keep digging until there's no more Chocograph left. The last Chocograph you will get is Chocograph #4, which will let Choco gain the Reef Ability.
Get your Reef Ability first.
Go to Chocobo's Lagoon. keep digging until there's no more Chocograph left. The last Chocograph you will get is Chocograph #12, which will let Choco gain the Mt(Mountain) Ability
Get your Mt Ability first.
Go to Chocobo's Forest. Keep digging until there's no more Chocograph left. The last Chocograph you will get is Chocograph #14,which will let Choco gain the Ocean Ability.
Get your Ocean Ability first.
Go to Chocobo's Lagoon. Keep digging for the remaining Chocographs and Chocograph pieces. Once you have all the six Chocograph pieces,
Chocograph #20 will appear, which will let Choco gain the Sky Ability.
Get your Sky Ability first.
Solve the 'mystery' of the six Chocograph pieces. Find Chocobo's Air Garden.
Dig in Chocobo's Air Garden to find the last three Chocographs.
Maybe, it is the time to search for the Dead Pepper treasures. Or you might visit to Fat Chocobo in Chocobo's Paradise.