Welcome to YorkieTalk.
Glad to hear that your little guy is coming along and making great strides with potty habits.
I recommend having your vet check out his rear end. Anal glands can get infected or impacted and sometimes rupture. Could also be another problem involving the anus and colon. Does he have difficulty pooping?
Be sure to check his anus daily to make sure it is clean. The smaller the dog, the more likely they are to have a little something left over that can cause problems. I have big boys (7 and 8 pounds), but I still check them every day because they are in full coat.
I am an advocate of not manually expressing glands unless absolutely necessary. Frequent manual expression can cause more problems than it solves. A dog's stools should be firm and large enough to express the glands naturally. If your dog's stools are a bit on the soft side or too small, then you may want to evaluate diet.