Preheat the oven to 350°. Line a rimmed baking sheet with parchment, Silpat, or foil and spray with non-stick cooking spray.
Place the tortillas on the pan and bake them for 3-5 minutes or until lightly crisped, flip over and bake for an additional 3-5 minutes until both sides are lightly crisped. Remove from the oven and set aside.
In a large skillet, cook beef, onion and garlic over medium-high heat until beef is browned and onion is tender. Drain grease. Stir in chili powder, cumin, salt, pepper, and cayenne.
Place two of the prepared tortillas side by side on baking sheet, and cover with a layer of refried beans. Scatter half of the seasoned ground beef over each tortilla, and then cover with a second tortilla.
Bake 10 minutes. Remove the baking sheet from the oven.
Spread salsa on top of each top tortilla stack. Top with cheeses, tomatoes, green onions, and jalapenos.
Return the pizzas to the oven, and bake for 5 to 10 more minutes, until the cheese is melted. Remove from the oven, and let cool slightly before slicing each one into 4 pieces.