Bring a pot of water to a boil add 1 tablespoon salt to it
Add 1 box macaroni and boil until al dente (around 10-12 minutes)
Slice onions, dice jalapenos, and cut bacon into 1/4 inch pieces
Cook bacon on medium high until crisp (about 10 minutes) and set aside
In the same pan your bacon was in, add the onions, sugar, and vinegar, and caramelize them
Once onions are caramelized, add jalapenos
Remove onions and jalapenos from pan and set aside
Turn heat down to medium
Preheat oven to 350°F
Microwave butter for 30 seconds and mix in flour to make a roux, and then add roux to pan
Add milk, stirring constantly
Once roux has bloomed, add Parmesan and stir to combine
Turn heat off and fold macaroni into the pan, coating all pieces
Add onion, pepper, bacon mix, and half the cheese, folding together to incorporate
Top with the remainder of the cheese
Bake for 30 minutes
Remove and serve