To speed up the process, I cook the potatoes in the microwave, then cube once cooled. However, by all means you cook in oven.
Cook bacon in skillet on stove or microwave. Drain grease of, then chop or crumble and set aside.
In a soup pot, melt the butter over medium heat. Whisk in flour unitl smooth. Gradually stir in milk, whisking constantly until thickened. Stir in potatoes and onions. Bring to a boil, stirring frequently.
Reduce heat, and simmer 10 minutes. mix in bacon, cheese, sour cream, salt, and pepper. Continue cooking, stirring frequently, until cheese is melted.