I always put registration marks on my top and back in the seam allowances. I fold the back in half, then in half again and mark the fold marks with a pencil. You do the same with the top. Since the back is supposed to be bigger than the front, you make sure the marks are aligned as you sandwich. (I make sure my batting is slightly smaller than the back so I can still see my marks) I haven't done a pieced back other than a seam but it is best to get that running straight as well.