Preheat the oven to 350°F (175°C). Bring the water and wine to a boil in a 5-quart saucepan. Add the clams, discarding any that fail to close to the touch. Cover, return to a boil, and cook for 5 minutes.
Uncover, remove any open clams with a slotted spoon, and then re-cover and continue to cook for 3 to 4 minutes longer, or until the remaining clams open. Remove them with the slotted spoon, discarding any that failed to open.
When the clams are cool enough to handle, remove the meats from the shells and reserve the bottom shells. Mince the clam meats. Rinse and dry the reserved shells.
Combine the minced clams, panko, saltines (if using), and egg in a bowl and mix well. Melt the butter in a skillet over medium heat. Add the yellow onion and saute for 5 minutes, or until lightly browned. Remove from the heat and add the sauteed onion to the clam mixture along with the scallions, parsley, salt, Bell's Seasoning, Old Bay Seasoning, black pepper, and cayenne pepper. Mix well.
Spoon the clam mixture into the reserved clam shells, dividing it evenly, and place the stuffed clams on a baking sheet. Bake for about 30 minutes, or until the tops are lightly browned.
Serve hot.