Overworld travel takes place entirely on the player's airship. The world is at first divided by impassable "sky rifts" which bar the player's passage. Throughout overworld travel, unavoidable random encounters occur as in the dungeons. These battles take place on the deck of the airship and are otherwise identical to their dungeon-based counterparts. Later in the game, however, an advanced mechanism is discovered for the player's ship which allows it to rise above the upper cloud layer and sink below the lower cloud layer of Arcadia, presenting two ways to avoid these encounters, and also provides the player the means to pass through sky rifts. In addition, ship-to-ship combat can occur whilst traveling through the overworld; however, the majority of these are unavoidable boss fights which advance the storyline. Random ship-to-ship battles can occur, but they are rare and avoidable.
Text from Wikipedia.org