Preheat your oven to 400 degrees F.
Heat olive oil in a skillet. Add diced onion and garlic. Saute for 2 minutes, until it is fragrant and onion has softened.
Add minced chicken and cook it for 4-5 minutes, until it no longer looks pink and is cooked through. Break big lumps of meat with a wooden spoon in between.
Add 1.5 cup Marinara sauce, rice, Italian seasoning and red pepper flakes(if using). Mix well. Make sure not to cook the mixture too long, else it will turn dry.
Add 1 cup mozzarella and parmesan cheese. You can also add a handful of chopped Italian Basil if you prefer. Mix well.
Cut peppers into half lengthwise. Remove the core and seeds. For the peppers to sit perfectly in the dish, trim a thin slice to get a flat bottom.
Arrange the peppers cut side up in an ovenproof baking dish, large enough to hod the peppers.
Stuff each pepper with the filling. Top each with a tablespoon of marinara sauce. Sprinkle the remaining mozzarella cheese on top.
Slowly add 1/4 cup of stock or water to the bottom of the pan.
Cover with aluminium foil. Bake it covered for about 30-35 minutes.
Remove the foil and bake it 5 minutes more on the upper rack of the oven until the cheese is bubbly.