So i have created a Square class, created a 2D array in my "NormalMode" class like this:
Square[][] square = new Square[4][4]
and initialized it with the 2 nested for loops. Now that i have this, how can i run a method from my Square class for all the square objects in the array at the same time?
Use another pair of loops, or use a static method if the method is independent of the Square instances (i.e. if the method doesn't modify or access any instance fields).
If you don't want a static method and you only want the method to be executed once you should put the code into the constructor, or call it from there.