Soak the beans for several hours (preferably overnight), drain and boil in fresh water until they begin to soften.
In a large pot, heat the olive oil and sautee the peppers and onions for about 6 minutes. Add the apaki or syglino (or the kind of smoked pork you're using), and sautee for a further 2 minutes. Drain the beans and add to the pot, together with the tomato. Mix well. Add the stock or water and bring to the boil.
Once boiling, lower the heat, add the thyme, salt and pepper, and simmer half-covered for 40-50 minutes, until the beans are done and the sauce is thick. Add a little water, when needed.
Serve in deep bowls, with a little olive oil and parsley, if you like.