I would say the Orbs factor about one third to one fourth of your overall ranking. The other elements are stylish points, clear time and damage received. Your ranking will suffer if you choose to continue or if you use an item. In the harder difficulties, the item penalty is not as severe. Choose automatic if you want easy stylish points. But as you become familiar with the combat system you will be pulling out SSS rankings with ease.
Try to make each run through a stage better than before and don't worry about S ranking stages until you at least complete the game once. I got S ranks just by playing the game without any intention of getting them. For Nero, get the Max Act ability as soon as possible as well. Also upgrade the Blue Rose to the max and learn all his Red Queen Combos and tack on the Air Hike Speed, and Snatch 2. For me those were essential skills.