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

Yes every positive number has two square roots, i.e. 25 gives 5 and -5

but when you are looking at a square window, its lengths are all the same and also the length has to be positive. You cannot have -5 cm. There is no such things as a negative length which is why we take the positive one only.  So if the surface area of a square window is 25cm². Then its length is √25 = 5 cm (or -5cm but again you cannot have a negative length, thus you only take the positive one).

Some math problems like this you have to think about if you can have a negative answer. in this case no, but other problems can sometimes have a negative answer.

Hope this helps :P