Preheat oven to 400ºF. Trim the top third of the jalapeños lengthwise, leaving the stem intact. Reserve the tops. Using a demitasse spoon or other small tool, scoop out the seeds and the ribs from all the peppers, making 12 "boats." Chop all of the trimmed pepper tops and reserve.
In a mixing bowl, combine softened cream cheese, grated onion, garlic, salt, pepper, shredded cheeses, cilantro and cumin. Add in finely chopped jalapeños to your taste -- I usually use about half of the total amount, reserving remaining jalapeño for other recipes.