Drain and rinse the beans after their overnight soak. Then place them in a large saucepan and cover with an inch or two of water. Bring to a boil and simmer until the beans are cooked through and just tender. This can take anywhere from an hour to two hours (potentially more) depending on your beans, but do your best to avoid overcooking. Remove from heat, salt the beans (still in bean broth) with about a tablespoon of salt - enough that the bean liquid is tasty but on the salty side. Let the beans sit like this for ten minutes or so before draining and setting the beans aside.
In the meantime, place the 2 tablespoons olive oil, red pepper flakes, couple pinches of salt, and chopped garlic into a cold medium saucepan. Stir while you heat the saucepan over medium-high heat. Saute just 45 seconds or so until everything is fragrant - you don't want the garlic to brown. Stir in the tomatoes and the fresh oregano and heat to a gentle simmer, this takes just a couple minutes. Remove from heat and stir in the adobo sauce - carefully take a taste (you don't want to burn your tongue)...If the sauce needs more salt add it now, more chipotle flavor? Go for it. Set aside.
Serves about 6.