FIrst make sure that your side measurements are the same and your end measurements are the same on your backing. Once you lay your backing on the flat surface/floor, use masking tape to hold the corners in place. Then take a tape measure (you'll need a carpenter's one for this because of the length) and measure diagonally, corner to corner. Adjust the masking tape until the two diagonal measures are the same. Also make sure there are no wrinkles in the backing. I usually use a few pieces of masking tape around the sides just to hold things in place.
Now lay on the batting. I like to unroll my batting and let it sit, draped over a bed or on the floor for a day or so, to let it 'relax'. If it is really really creased and compressed, I have thrown it into the dryer on low for a few minutes. I try to make sure that my batting is smaller than my backing fabric but larger than my top.
Now it is time for your top. Because you know that your backing is squared up and straight, you can use it to help you position your top. But before you pin it all together, get out that carpenter's measuring tape again, and check the diagonal measurements for the top. Again, they should be the same. Once you have adjusted things so that they are, use a bit more masking tape on the corners and sides to hold things in place, then have at it with the pins or basting thread.
Finally, carefully remove the masking tape and quilt your quilt.