Under the broiler or over a gas burner, char the peppers, turning occasionally, until blistered all over. Place in a bowl, cover with plastic wrap and let cool 15 minutes. Peel the peppers, then make a lengthwise cut down one side of each. Carefully open up the peppers, forming boats, and remove the seeds. Arrange the peppers, cut side up, on a large, rimmed baking sheet.
Meanwhile, in a small saucepan, heat the oil, one turn of the pan, over medium-high. Add half the onion, half the jalapeno, the garlic and the cumin. Season with salt and pepper and cook, stirring often, until the onions soften, 2 to 3 minutes. Mix in the beans and water. Bring to a bubble, reduce the heat to low and let the filling simmer while you make the salsa.
In a medium bowl, mix the remaining onion and jalapeno with the chopped tomatoes and cilantro. Season the salsa with salt.
Preheat the broiler if you did not use it to char the peppers.
Fill the peppers with the bean mixture, then top with the chips, salsa and cheese. Broil until the cheese melts and the edges of the chips brown, 2 to 3 minutes. (The peppers will look like they are filled with nachos.) Sprinkle with the scallions.