In a large pot, combine the chicken stock, water, and 1 tablespoon salt, and bring to a boil over high heat. Add the pasta and cook until tender but still firm to the bite, stirring occasionally, about 8 to 10 minutes.
While the pasta is cooking: Heat 1/4 cup of the oil, over medium-high heat, in a large Dutch oven. Add the onion, season with salt and pepper, and cook until soft, about 5 to 7 minutes. Add the garlic and cook for 1 minute longer. Add the Marsala wine and grape tomatoes, and cook for 1 minute, scraping the brown bits that cling to the bottom of the pan with a wooden spoon. Add the clams and mussels to the pan. Cover the pan with a tight-fitting lid and cook until all the shellfish have opened, about 5 to 8 minutes. Discard any unopened shellfish.
Using tongs, remove the shellfish from the pan and reserve. Drain the pasta and transfer to a large serving bowl. Pour the shellfish cooking liquid over the fregola. Add the remaining olive oil and 1/4 cup of the parsley and toss. Place the reserved shellfish on top of the fregola and garnish with the remaining parsley.