Add warm water, 1 tablespoon molasses, and yeast to a small bowl and whisk until dissolved. Allow to sit until foamy, about 5 minutes.

Whisk together flour and salt in a stand mixer bowl. Combine the water and yeast mixture with the flour on low speed until a shaggy dough forms. Scrape down the sides and increase speed to medium as needed until the majority of the loose flour is incorporated.

Increase speed to medium high and knead for 10 minutes until the dough is flexible and bouncy.

Roll the dough into a tight ball, place in a clean bowl, and cover with plastic wrap. Allow to rise in a warm place until doubled in size, about 60–90 minutes.

Prepare two baking sheets generously sprinkled with cornmeal.

Punch down the risen dough and divide it into pieces weighing 4 ounces each.

Roll each piece into a ball, push through the center to make a hole, and stretch the bagel to about 4 inches across. Place shaped bagels on the baking sheets and cover with plastic wrap.

Allow bagels to proof in the refrigerator for 12–18 hours.

Preheat the oven to 450°F (230°C) with pizza stones on racks for at least 30 minutes.

Fill a large pot halfway with water, bring to a boil, and add molasses until the water is dark brown.

Remove bagels from the refrigerator and gently place into the boiling water, boiling for 30 seconds on each side. Remove with a slotted spoon and top each bagel with 2 tablespoons of cheddar cheese. Place on a wire rack to cool.

Transfer boiled bagels to the hot pizza stones, leaving space between them, and bake for 15–19 minutes until golden brown. Let cool on a wire rack.