How to Make It
Peel the sweet potatoes and cut them into 1-inch cubes. Put the sweet potatoes in a large saucepan and add cool water to cover by 1 inch. Set the pan over medium-high heat and bring to a boil. Reduce the heat to low to maintain a gentle simmer and cook until the sweet potatoes are fully tender, about 15 minutes. Drain the sweet potatoes, reserving the cooking liquid.
For a perfectly smooth puree, first pass the sweet potatoes through a food mill or press them through a potato ricer, discarding any pulpy, stringy flesh that remains. Give the milled sweet potatoes a good stir with a spoon, and add a tablespoon or two of cooking liquid if the puree seems dry or tacky. For a coarser puree, simply mash the sweet potatoes with the back of a fork or a potato masher. They will collapse into a relatively smooth mass that should not require additional liquid to remain moist. Set aside 2 cups of puree for the fish pie; reserve the rest for another use.
Preheat the oven to 375°. Cut the cod into 1-inch pieces. Peel and devein the shrimp. Pick over the scallops for bits of shell, and if there is a tough band of muscle adhered to one side of each scallop, remove it. Refrigerate the seafood until ready to use.
Melt 2 tablespoons of the butter in a medium saucepan set over medium heat. Add the onion and cook, stirring, until translucent and soft, about 5 minutes. Pour the milk into the pan and add the bay leaves and thyme sprigs. Bring to a gentle simmer, stirring often. Stir 1/2 teaspoon of salt into the milk.
Poach each type of seafood individually: Place the cod in the simmering milk and cook until the fish is nearly cooked through, 1 to 2 minutes. Lift the cod from the milk with a slotted spoon and place it in a 2- to 3-quart casserole dish. Add the scallops to the milk and poach until opaque, about 30 seconds. Lift from the milk with a slotted spoon and add to the dish with the fish. Add the shrimp and poach until they just begin to curl, about 1 minute. Lift them from the milk with a slotted spoon and add them to the dish. Use your hands or a fork to flake the cod into bite-size pieces. Season the fish with 1/2 teaspoon salt and 1/4 teaspoon pepper.
In a small bowl, mash 2 tablespoons of the butter with the flour. Remove the bay leaves and thyme sprigs from the milk. Bring the milk to a simmer once again and whisk the butter mixture into the milk until no lumps remain. Reduce the heat to low and simmer, stirring, until the mixture thickens, about 5 minutes.
Pour the béchamel over the fish in the casserole dish. Add the chives and fold gently to combine everything. Taste the filling and adjust the seasoning with salt or black pepper, if needed.
Reheat the 2 cups of sweet potato puree in the microwave, stirring every 30 seconds, or in a pot, stirring constantly, until warm. Stir the remaining 2 tablespoons butter into the sweet potatoes until it melts and season lightly with salt. If desired, transfer the warm sweet potato puree to a piping bag fitted with a star tip. Pipe or spread the puree over the filling, sealing the edges.
Bake until the filling is bubbly and the topping is browned, about 20 minutes. Let stand for a few minutes before serving.