Heat a large skillet over medium heat . Dice pepper and add to hot skillet. Saute for 1-2 minutes; add beef. Cook and stir to break up beef into crumbles. Cook until no longer pink. Add salt and pepper to the meat. Stir in marinara and remove from heat.
Preheat oven to 400 degrees F.
Transfer cauliflower rice to a microwavable bowl and loosely cover with a paper towel. Microwave on high for 5 minutes. Once the cauliflower rice has cooled, transfer to a dish cloth, and squeeze out as much of the liquid as possible. Place the dried cauliflower to a bowl and mix in the eggs and seasonings.
Spray muffin tin with cooking spray. Scoop approximately 2 tablespoons of cauliflower mixture into each muffin cup and press firmly, forming a cup to fill. Bake cauliflower cups for 15 minutes or until edges are golden brown.
Remove cauliflower cups from the oven and add 2 tablespoons of beef mixture to each. Sprinkle with cheese. Bake for an additional 15 minutes or until cheese is melted.
Freeze remaining in an airtight container or freezer bag. Reheat by cooking in a 375 degree F oven for 15 minutes or until hot.