There is actually more than one way of doing it.
How to make ships go on areas of the map
How to make ships move around on islands in the sea:
X1
Z1
X2
Z2
The X1 means your first x is equal to equation and X2 is your second one. Same with the Z ones. Using your math's skills, count along the gridsquares to the map and insert the equations (in the boxes, you enter the number you want the letter to equal to) to form a square.
If you find me nattering on a bit, you can insert the trigger on a blank 200 by 200 sized map (1 gridsquare per 2 metres) and experiment. I inserted some default numbers into the trigger that works beautifully on a 200 by 200 map. Experminet till you fully understand how to use it.
Anway, when you have made your square, playtest the map. If your water was less than 0 metres high, a square island should have formed. You will find that you can move your ships across them too! However, as you might have suspected, because ships can move across it, land units cannot because like the last example, the game still thinks that there is water there. If you want a different shape, simply insert more than 1 square and overlap them. To make the island more realistic, use the: zSmoothen area of map trigger to smoothen the land out and make it more realistic. If you find this method too complex, stick to method one.
Secret areas of RPGs where you can get to a special reward by sailing over land that looks exactly like it's surroundings.
Pit of doom type maps but with ships - see screenshot above for the example. To make land impassable by ships, simply raise land out of the water in the editor manually before playtesting. (for the screenshot, I had a ring of raised land around the arena to prevent ships sailing down the cliffs when the game started.
Make a sea battle but on dry land! This could be a very amusing map since the entire game would be ships sailing around on a completely dry lake!
Simply just to show off and make people go wow and how do you do that!
And there are many other ideas that have not just come straight off the top of my head as I was writing this guide.
Have fun and enjoy experimenting and making ships go on land!