Preheat the oven to 350 degrees F (175 degrees C).

Bring water to a boil over high heat. Add sausage links; reduce heat to medium and simmer for 10 minutes. Remove links from broth; reserve the broth. Remove casings from sausage.

Bring broth back to a simmer and add quahogs; cook until they open, 5 to 10 minutes. Remove quahogs; reserve the broth. Remove cooked quahogs from the shells. Separate the shell halves. If necessary wash the shells.

Place sausage and quahog meat into the bowl of a food processor; process until chopped, about 12 seconds, depending on your processor. Scrape mixture into a bowl. Add chopped onion to the processor and blend about 5 seconds; stir into meat mixture.

Make stuffing according to package directions, using margarine and substituting the sausage/clam broth for water. There may be more broth than you need.

Mix stuffing and sausage/clam/onion mixture. Spoon filling into empty clam shell halves and top each with a small pat of butter (about a third of a teaspoon).

Place the shells on a baking pan; bake in the preheated oven until toasty brown on top, 15 to 20 minutes.