Scooting is definitely a sign of something going on with the anal glands, which could be the origin of his stool problems, or could be caused by his soft stools. Usually takes firm stools to empty the glands.
A full cup of RC a day sounds like a lot for a 5 pound dog. On the RC website, if I am reading this correctly, they recommend 3/4 cup a day for a high activity dog weighing 6.6 pounds:
Yorkshire Terrier / BREED HEALTH NUTRITION? / Dog Products / Products / Products / Home Royal Canin USA - Royal Canin
Being 13 months old, your pup is at the age when you want to start cutting food back a little. Puppies can generally free feed, but at 1 year is when you want to establish the adult portion.
I don't want you to think I was suggesting your dog is overweight. I was just thinking about my experience with my boys, how they have had some stool problems from overeating, usually when we get too generous with fresh chicken supplements to their kibble, or too many kibble rewards adding up to an extra meal. It's so easy to do.
I hope you can figure out your little guy's problem and get him back on track.