Line a plate or rimmed baking sheet with parchment paper and set it aside. In a large bowl, place the masa harina, and salt. Mix to combine. Create a well in the center, and pour in about 10 fluid ounces of the water. Mix to combine. The dough should not be sticky, and not dry, but should be a bit tacky to the touch. Add more water by the tablespoonful, mixing to combine, until there are no crumbly bits. The dough is easier to work with a little too wet than a little too dry. Cover the bowl and set it aside for 5 minutes to allow the masa to absorb the liquid.
While the dough is resting, in a separate, medium-sized bowl, place the beans. Add the desired spices to taste, and mix to combine. Place the cheese in a small bowl beside the beans. Place a small bowl with warm water beside the cheese.
Check the dough. If it appears too dry, add a tablespoon of water, wet your hands in the water bowl, and work the water in to the dough. Once the dough is ready, divide it into 6 even parts. Take each piece of dough and roll it into a ball with wet hands. Then, a rhythmic motion, pat the dough between wet palms until it flattens. If it splits along the edges, just press it back together. Pupusas are not meant to rise when cooking, so a tight seal around the edges is not necessary.
Press the center of the flattened dough gently into the palm of your hand to create a well for the filling. Add a spoonful of the black beans to the well, and top with a couple tablespoons of grated cheese. The dough will be nearly covered with filling. Then, with the hand that is cradling the pupusa, begin to close the edges of the dough toward the center, rotating the ball in your hand as you work. Your free hand should help to thin the dough a bit to cover the filling. Once the filling is covered with the dough, pat the dough flat again between moistened palms. Place on the lined plate or baking sheet, and repeat with the remaining pieces of dough and filling.
Heat a 12-inch cast iron pan over medium-high heat. Place as many pupusas as will fit without crowding one another in the pan, and allow to cook on one side for about 3 minutes, or until the underside is no longer shiny and beginning to brown. Flip the pupusas with a metal spatula, and allow to cook on the other side for another 3 to 4 minutes. Serve warm.