Place red beans into a large container and cover with several inches of cool water; let soak, 8 hours to overnight. Drain and rinse.
Add celery, onion, bell pepper, and garlic to a blender and process until just shy of a puree.
Add vegetable oil to a saucepan or stockpot over medium heat. Cook and stir vegetable mixture for 5 minutes. Add thyme, oregano, black pepper, cumin, and cayenne pepper. Cook, stirring regularly, for 2 minutes more.
Add 6 cups water, the beans, liquid smoke, and bay leaves. Stir to combine and turn heat up to high. Bring to a boil, reduce heat to low, and let simmer until beans begin to fall apart, 2 to 3 hours.
Bring remaining water and rice to a boil in another saucepan. Reduce heat to medium-low, cover, and simmer until rice is tender and water has been absorbed, 20 to 25 minutes.
Pour most of the cooking liquid from the beans into a bowl and reserve. Remove bay leaves. Mash about 1/3 of the beans, adding as much of the reserved liquid as necessary to reach preferred thickness. Mix with the unmashed beans and season with salt. Serve beans over rice.