Here's the locations of the Magic Bean Squares.

Lake Hylia by the laboratory.
Desert Colossus by the temple.
Gerudo Valley by the bridge.
To the left of the entrance bridge to Kokiri Forest.
By the Kokiri shop.
Lost woods - trail to it: right, left, right, left, and left.
Zora's river by the bean selling man.
Kokariko graveyard at the top-back-left corner.
Death mountain trail at the foot of dodongo cavern.
Play the Bolero of Fire to warp into the death mountain crater and the square will be right near the point of arrival.