Father-son project: Drawing on a grid
To make them square:  

var size = Math.max(window.innerWidth,window.innerHeight)/200;
var xbound = Math.floor(window.innerWidth/size);
var ybound = Math.floor(window.innerHeight/size);


Simply use xbound and ybound as the upper limits in the for loops.

Try to use CSS where you can.

Additionally, your script loads very slowly because of the excessive DOM manipulation. Rather than adding each element to the page one by one, create a single object and then paste that in one go. Just add up the html code with the += operator before inserting it into the page.