Preheat the oven to 400 degrees F (204 degrees C).
Arrange the chicken breasts in a single layer in a stoneware dish. Season both sides with salt and pepper.
Cut 6 slits in the top of each chicken breast in the short direction, about ½ inch (1.27 cm) apart, cutting about ¾ of the way down but not all the way through to the bottom.
In a medium bowl, mash together the cream cheese and shredded cheddar. Stuff the cheese mixture into the slits.
Stack the cooked bacon slices and make 2 cuts to cut each slice into 3 pieces, which would be approximately the width of the chicken breasts. (If you don’t have any cooked, you can cook bacon in the oven like this while you prep the chicken.) Stuff the bacon slices into each slit, 6 small pieces per chicken breast.
Stuff the jalapeno slices into each slit, 6 slices per chicken breast.
Bake for about 25 minutes, or until internal temperature reaches at least 163 degrees F (71 degrees C). (Note: The baking time will vary depending on the size of your baking dish. If the chicken pieces are not touching each other, they will be done faster.)
Remove from the oven and let the chicken rest for 5 minutes before serving. Internal temperature will continue to rise a few degrees -- use a meat thermometer to ensure it has reached 165 degrees F (74 degrees C) before serving.
Sprinkle with fresh chives right before serving, if desired.