Make filling: Place chicken breast, half the onion, and the bay leaf in a medium saucepan. Cover with cold water, and bring to a boil over medium-high heat. Reduce heat to medium-low, and poach until chicken is cooked through, about 15 minutes. Transfer chicken to a plate; reserve 1 cup cooking liquid, and discard onion and bay leaf. When chicken is cool enough to handle, shred meat from the bone with a fork; set aside.
Roast poblano chile directly over a gas flame, turning as each side blackens and blisters. (Alternatively, roast chile under the broiler.) Transfer to a bowl, and cover with plastic wrap; let steam 10 minutes. Remove plastic wrap; peel off and discard blackened chile skin. Remove stem, seeds, and ribs; discard. Slice chile into 1/4-inch strips; set aside.
Finely chop remaining onion. Heat 2 teaspoons oil in a medium saucepan over medium heat. Add chopped onion and garlic; saute until soft and translucent. Stir in cumin and canela; cook 1 minute. Add shredded chicken, tomatoes, chipotle, poblano, and reserved cooking liquid. Cook over medium-low heat, stirring occasionally until liquid has thickened, about 25 minutes. Remove from heat. Season with salt and pepper; stir in cilantro and pepitas. Set aside to cool.
Make empanadas: Break off a 1 1/2-inch ball of empanada dough. On a clean work surface, roll dough into a circle about 1/8 inch thick. Using a 3 1/2-inch cookie cutter, cut out a round of dough. (Or use an inverted glass as a guide, cutting around it with a sharp paring knife.)
Place 1 teaspoon filling in center of each round; sprinkle with cheese. Using a pastry brush, moisten edges of dough with water; fold dough over to seal, pressing gently. Crimp edges with a fork; set aside. Repeat with remaining dough. Gather scraps and reroll. (Only do this once, to avoid toughening the dough.)
Pour remaining oil into a medium saucepan; oil should be 2 inches deep. Place over medium heat until oil reaches 375 degrees on a deep-fry thermometer. Working with a few empanadas at a time to avoid overcrowding, fry until golden, turning once, about 1 minute. Using a slotted spoon, transfer to drain on a paper-towel lined baking sheet. While still hot, sprinkle tops with sugar. Serve immediately with crema pura or cream on the side, if desired.