In a large bowl, combine grated cheeses and set aside.
In a medium saucepan, melt 6 tbsp butter over low heat. Add the flour and stir to combine. Cook, stirring constantly, for 3 minutes. Increase the heat to medium and whisk in the milk very slowly to avoid lumps. Cook until thickened, 4-5 minutes, stirring frequently.
Remove from heat, then season with salt, pepper, minced garlic, jalapeno juice and chopped jalapenos. Stir in about 1/3 of the grated cheeses until cheese has melted and sauce is smooth. Cover and set aside.
Cook pasta until very al dente. Drain the water and return to the pot. Add the cheese sauce and stir until well combined, then set aside.
Place 1/2 of the pasta in a 9 X 13 baking dish. Top with the cream cheese cubes. Top with 1/2 of the remaining grated cheeses. Pour the remaining pasta over cheese layer and top with the last of the cheese.
Melt the remaining butter in a large skillet over medium low heat. Add the panko bread crumbs and stir to evenly cover the bottom of the skillet. Let cook until the bread crumbs have absorbed all of the butter and are lightly toasted, 4-6 minutes, stirring frequently. Remove from heat and stir in the crumbled bacon. Sprinkle topping evenly over the top of the macaroni and cheese. Bake at 350 degrees, for 40-45 minutes, or until the macaroni and cheese is bubbly and hot and the top is golden brown.
If the top browns too quickly, tent the baking dish with foil. Remove from the oven and allow to sit for 5 minutes before serving.