Warm oil in a large skillet over medium high-heat. Add beef and sprinkle with ½ tsp salt, ½ tsp pepper, and red pepper flakes. Cook beef until cooked through, stirring occasionally. Drain if necessary.

In a medium bowl, combine ricotta cheese, ½ cup Parmesan cheese, ½ cup shredded cheese, egg, ½ tsp salt, and ½ tsp pepper. Mix until well blended.

Fill a resealable bag with the ricotta mixture. Clip off the tip of the bag and fill the manicotti shells until no more mixture fits. Repeat until all shells are filled.

Add tomatoes, sauce, paste, Italian seasoning, and water to the skillet. Turn heat to high. Place stuffed manicotti into sauce, pressing down to submerge, and spoon sauce over the shells.

Cover the skillet to bring to a boil, then reduce to simmer. Cook covered until pasta is al dente, about 10 minutes.