It depends on if you like your baked beans soupy, saucy, or with a thick rich sauce.  Many cooks don't drain them because they want the extra liquid.  If you are going for a soupy baked bean, you'll want to keep the liquid.  If you like this dish with a saucy consistency, you can drain half the cans.  For our recipe, we drain all the liquid, as we like the sauce to be thick.  Draining and rinsing will also reduce the sodium and gas in the beans.