Bring a large pot of water to a boil. Salt the water and cook the pasta until al dente according to package instructions; drain and set aside.
Meanwhile, heat a medium saucepan over medium heat. Add the diced bacon and cook, stirring occasionally, until browned and crisp, about 10 minutes. Transfer to a paper towel-lined plate to drain, leaving 2 tablespoons bacon fat in the saucepan.
Add 3 tablespoons butter, the chopped jalapenos, onion, and garlic to the saucepan and cook until softened, about 7-10 minutes.
Add the flour and cook, stirring, for 1 minute.
Add the milk and bring to a boil, stirring constantly, then reduce to a simmer and cook for 3 minutes more, stirring occasionally.
Remove from heat and add the cheddar, pepper jack, and cream cheese; stir until melted and combined. Add salt and pepper to taste.
Stir together the cooked pasta with the cheese sauce and bacon bits, stir to combine, and transfer to a casserole dish.
Melt the remaining 3 tablespoons butter and toss with the panko breadcrumbs to coat. Sprinkle over the casserole.
Broil for 2-3 minutes until golden brown and crispy.