Spread a kitchen towel on the counter. Use the jar lifter to remove the warm jars from the canner, drain, and line up on the towel.
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 small pot you used to warm your lids.
Use the canning funnel and ladle to fill the jars with the baked beans and bean liquid leaving 1-inch headspace. Aim for about 1-inch of the bean liquid over the beans while maintaining a 1-inch headspace from the rim of the jar. This seems to help prevent liquid loss during the pressure canning process.
Run the bubble popper through the jar to remove air bubbles and wipe the rims. Use the magnetic lid lifter to lift lids out of the warm water, center lid on the jar, and screw on band until it is fingertip tight.
Use your jar lifter to place the jars into pressure canner on the canning rack. Leave space in between the jars. Once the jars are all in canner, adjust the water level per your pressure canner's instructions. If adding water, use the hot water from the small pot you used to warm your lids.
Process pint jars of baked beans at 10 pounds of pressure for 80 minutes (1 hour and 20 minutes) at altitudes of less than 1,000 ft. Follow the directions for your pressure canner and adjust processing time for your altitude if necessary.
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.
Spread a dry kitchen towel on the counter. Use a jar lifter to lift jars carefully from canner and place on the towel.
Let the jars cool undisturbed for about 12-hours. You should hear a "ping" as the jar lids seal.
After 12-hours, check to be sure jar lids have sealed by pushing on the center of the lid. The lid should not pop up. If the lid flexes up and down, it did not seal. Refrigerate the jar and use up within a few days.
Once cool, remove the screw on bands and wash the jars. Label, date, and store your jars in a cool, dark place and use within 12-18 months. Yields about 9 pints of Boston Baked Beans depending on the size of your beans.