If every positive number has two square roots and you can find the length of the side of a square window by finding a square root of the area, why is there only one answer for the length of a side?

Because when you're working with real wood and tools and glass, there's
no such thing as negative length. 

One of the square roots of every number is negative.  When you're working with
a real window, the area still has two square roots, but you ignore the negative
one, because it has no physical significance in the real world and it can't help
you, so it's no good for anything.