Char peppers under the broiler, turning occasionally or over an open flame on a gas burner. Once charred and blistered, place in a bowl to cool. Peel peppers then slit them lengthwise on one side and remove seeds, forming pepper boats. Arrange on a baking sheet.
Meanwhile, heat oil in a small pan over medium-high heat, add 1 jalapeño, half the onions, the garlic, salt, pepper and cumin, and stir 2-3 minutes. Add beans and thin with 1/4 cup water; bring to a bubble then reduce heat to low.