So, im 16years old and I run everyday. My height is currently 5'6 and my penis size is 5.5 inchs erected and 3.5 non... Will running or growing help it increase?

Your height bears no relation to the size of your penis, nor can any type of exercise or pills help to make it bigger. You are in the average range which is 4 to 7 inches erect. If it works as it should be happy with what you have. By 16 it's very unlikely to get any longer. Penis growth usually stops aroudn 15 or so. You also have to go by erection size, not flaccid size. The flaccid length varies at different times of the day as every man knows. If the flaccid penis looks small to you at times that just means the tissue is healthy and elastic.

Running will have no impact on the size of one's penis. And growth in height is also not directly tied to penis size increases. It's common for the penis to stop growing before final height is reached.