To get the Giant Squid Location Map, use Treasure Map 26: Found on Six Eye Reef – Take out all the cannons and boats in the area to make the chest containing the map appear. Use the Deku Leaf to get over to it and open it.
There are six different squids and each of them have a reward in defeating them. Then best way to defeat them is to use your boomerang to autolock on their eyes.
4-Eyed Squid(1): Great Fairy: 2X Magic Meter
8-Eyed Squids(3): 100 rupees
12-Eyed Squids(2): Heart Container