Why is 1/4" underlayment supposed to be parallel to the subfloor?
Most subfloor and underlayment sheet goods are manufactured with greater strength/stiffness on one axis. It may have longer wood strands in that direction, or it may have a greater number of plies with grain in that direction. For this reason it should be oriented perpendicular to framing members. 

You should stagger all joints. This may mean ripping a half sheet to begin an area, and may even mean cutting that rip into a quarter sheet. You wouldn't need to hit right at a 50% lap, but shoot for at least 12" or so on the long edge. Butt joints should occur over framing. 

You don't typically need to fill flaws in subfloor, but we had a standard practice of taking a drum sander to swollen OSB subfloor if it had been rained on several times during house framing. The edges swell more than the field, and that creates humps. Small gaps such as at T&amp;G joints don't require filling.