The archipelago campaign is the closest I've come to running a sandbox-style game. As soon as the party lands on the island they have one main task ahead of them, explore the entire archipelago. How they choose to go about this is their prerogative. But there is more to the island than just making a map of hills and trees. Depending on how the party chooses to fan out and search, they may miss a few adventure hooks I have laid out for them.
Part of the problem is the way overland maps are drawn in role-playing games. Unlike most maps that show landmarks and exact positions of things, more RPG maps are little more than hexagonal graph paper with markers in each hex to indicate terrain. A single hex can be anywhere from 100 feet to 10 miles wide. I'm using 1 mile hexes, but that still leaves a lot of room for a party to walk past a hook or macguffin. Since experience in this game will be awarded more on exploration and discovery than combat, the party will have to be thorough to avoid missing anything.
This works both for and against me. If the party just walks by the hook it gives me time to flesh things out while I throw random encounters at them, but it slows advancement down considerably and may get boring after a while. On the other hand if they choose to be through in searching every square mile of the island they should find everything, but again it will likely slow down while they explore every nook and cranny, and most of the time without finding anything.
My only solution will be to establish a short-term goal up front that will lead to clues about the island's origins and secrets. Hopefully it will allow the party to meet all their goals without railroading them.