Look at pictures of the finished model or depictions of the actual ship in artwork to determine what how the hull to the beakhead transition should appear. The idea is, you want to raise the low spots on the hull, not just remove the high spots except in very few areas. Use filler and sand to the desired shape using both cylindrical and flat sanding blocks. <-- USE THE RIGHT TOOLS!
Don't use your fingers and sandpaper, or the weaker of the two materials (either wood or filler) will wash away leaving only the stronger material proud, and you will continue to have ripples and flat spots in the surface, and perhaps create even more. Add filler around a bulge, and add filler to flat spots in order to raise low areas and smooth the overall hull shape. You don't want to only sand the high areas down, because you will sand through the planks somewhere and create a hole in the hull. Check to see that the shape is symmetrical port to starboard. When viewing the hull, use sunlight and look along the hull's surface at an oblique angle to look for waves, bulges, and flat spots. Looking directly at the hull won't show you much. Repeat filling/sanding until it looks correct.
