Here is what sometimes happens - the centers are aligned but the edges leave something to be desired:
My solution was to allow an extra 1/4 in border on each side of the finished square (i.e.: make a 4 1/2 in square rather than a 4 inch square.) . I then lined the center seams of the square up with intersection lines of the cutting mat and trimmed the four sides to have exactly two inches from the center axis on each side.
The result is a beautiful 4 inch square ready to be appliqued.
I also completed another "Comfort Quilt" for my local guild. One of my personal goals for my Vision Project with SAQA is to create 10 quilts before September 2011 for charity. I am on my second Comfort Quilt and now have it ready to hand in at our October meeting.