I have done both ways and parallel to the rollers is definitely the best way. If you have a seam running perpendicular to the rollers you end up with a problem - the double thick fabric builds up as you roll and so your backing is tighter where the seam is and looser far away from it, so it pulls your backing and that's when you get those pesky tucks in your backing.
Now, I never load a quilt backing with a seam perpendicular to the rollers if there is any other way to do it!