Boil a large, salted pot of water for the jumbo shells. Cook them al dente according to package directions.
Add the oil and onion to a skillet over medium-high heat and sauté for 4-5 minutes or until the onion is just starting to lightly brown.
Stir in the garlic and cook for 30 seconds.
Add in the ground beef, chili powder, smoked paprika, and cumin. Cook, breaking up the beef with your spoon as you go along, until the beef is browned and cooked through (about 8 minutes). If there's lots of excess fat, spoon most of it out.
Meanwhile, preheat the oven to 375F and move the rack to the top third of the oven. Grease a 9x13 baking dish and spread the salsa in an even layer on the bottom.
Take the skillet off the heat and stir in the sour cream and half the cheese (stir until it's evenly melted in). Season with salt & pepper as needed.
Rinse the shells under cool water and drain them thoroughly. To stuff the shells, take a small spoon and add the mixture into each shell. You should be able to stuff them fairly full. I add them to the baking dish one at a time as I go along.
Top the shells with the remaining cheese.
Bake, uncovered, for 20 minutes. You can then broil them for a few minutes to brown the cheese if you wish. Note: you can cover the baking dish with foil prior to baking if you like. I like to have some crispy bits, but if you want it all to be softer, I suggest doing that (take the foil off to broil, though).
Prep the toppings while the shells are baking.
You can top the shells while they're still in the baking dish or serve them and then top each plate as desired.