Remove the baked beans from the oven and give everything a good stir to combine. Pluck out and discard the bay leaves. The beans should be soupy in order for the heat to penetrate evenly though the jar. If you need to add water, use the hot water from the canner.
Spread a kitchen towel on the counter. Use your jar lifter to remove a jar from the canner. Pour out the water (save it for washing dishes), and place the jar on the towel. Keep the remaining jars in the canner, so they stay hot.
Place the canning funnel on the jar. Use a slotted spoon to remove the beans from the pan and fill the jar with beans to about 3/4 full. Ladle hot cooking liquid over the beans while maintain a 1-inch headspace. Remove air bubbles with the bubble popper, and wipe the rim with a damp towel.
Center a lid on the jar, place the band over the lid, and screw it on until fingertip tight. Use the jar lifter, and place the jar back on the rack in the canner. Repeat with the rest of the jars until the canner is filled, or you run out of beans.
Close the pressure canner and secure the lid. Leave the vent open, adjust the heat to medium-high, and bring the canner to a boil. Allow the pressure canner to vent for 10 minutes, then place weight on the vent.
Once the canner has reached the correct pressure (10 pounds for weighted gauge canner, and 11 pounds for dial gauge canners.), set a timer, and process pints for 80 minutes (1 hour and 20 minutes), and quarts for 95 minutes (1 hour and 35 minutes) at altitudes of less than 1,000 ft. Adjust for your altitude if necessary (see table below).
Adjust the heat as needed to maintain a steady pressure. When the processing time is complete, turn off the heat and allow pressure canner to de-pressure on its own (approximately 1 hour).
Once the canner is at zero pressure, wait 5 minutes, unlock, and remove the cover by tilting the lid away from you so that steam does not burn your face. Let the canner set for another 10 minutes to adjust to the change in pressure.
Spread a dry kitchen towel on the counter, and use the jar lifter to lift jars from canner and place on the towel. Keep upright, and don't tighten bands or check the seals yet. Let sit undisturbed for 12 to 24-hours to cool.
After 12 to 24-hours, check to be sure jar lids have sealed by pushing on the center. The lid should not pop up. If the lid flexes up and down when the center is pressed, it did not seal. Refrigerate the jar and use up within a few days.
Remove the ring bands, wash, label, date, and store in a cool, dark location (50 to 70 degrees F). Use within a year for the best quality. Yields 6 pints, or 3 quarts.