If you want your quilt to be as square as possible without "waves" in the borders it is best to do the sides first and cut the fabric for those sides on the selvage edge. That part of the fabric stretches the least. If it is not possible than do what you have to do. All of us have ended up with quilts that won't lay flat. Straight of grain does make a difference. It also helps if you starch your fabric. Another tip is to put the least stable fabric be it the quilt top or the border on the bottom when stitching. The feed dogs will ease it in.
Good luck.