I make beans by soaking overnight (especially lima's, and baby lima's, northern, black-eyed-peas - overnight is not necessary for split peas, and definitely not for lentils). At about 4 or 5 the next day, I drain and rinse well (prevents gas), then put in clear water with whatever recipe I'm using (smoked bone off a pulled pork shoulder, ham hock, whatever...), onions, carrots, bay leaf, etcetc... and bring to a boil then simmer for 1-2 hours. You can also cut up bacon and fry with onions (chowder style) in the pot, then put the washed beans and stuff in with water (or stock).
Anyway - I never had beans like this growing up in Boston, but my southern wife grew up with this - and it's the traditional way to do it. There are quicker ways, including simmering the beans for several hours, then draining, rinsing, and treating them as if they had soaked overnight.
Bean soups done this way are typically a winter meal - not especially good for a hot summer day. By the time the weather turns cold, we can't wait for the first pot of beans and cornbread - I've usually got a stock of smoked shoulder bones from the summer's barbeque that will last through the winter.