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?

That's a GREAT question ! 
The answer is:

Because the two square roots of a positive number are ...

           one positive square root
and 
           one negative square root.

As long as you're doing math, on paper, you can work with both of them.
But as soon as you start talking about windows or other physical things,
it's pretty silly to talk about a negative length.  When you're working with
real physical things, you usually just ignore the negative square root.