In the morning: place the lima beans in a Dutch oven or large pot, cover with water by about 2 inches, and let them sit for at least 6 hours and up to 8 to 10 hours.
About an hour before dinner: Add more water to cover the beans by about 1½ inches. To the pot, add the onion, salt, pepper, olive oil, bay leaves, and thyme, and bring to a boil. Then lower to a simmer, scraping off any foam from the surface as it cooks. Start checking for tenderness at about 40 minutes. You want them to still be holding their shape, but creamy in the inside.
Once tender, do not drain the beans. Pick out the thyme sprigs (they will just be leafless twigs) and scoop beans into serving bowls with a little of the bean broth. Finish with another drizzle of olive oil and serve with any combination of the suggested toppings, making sure that burrata is one of them.
