Place potatoes in large saucepan and cover with water by 1 inch. Bring to boil over high heat. Reduce heat to medium-low and simmer until potatoes are al dente and paring knife inserted into them still meets some resistance, about 3 minutes. Drain potatoes in colander and transfer to medium bowl. Let potatoes cool completely, about 30 minutes.

Add chopped clams and their juice, onion, 1 teaspoon salt, and pepper to potatoes and stir to combine. Transfer mixture to 1-gallon zipper-lock bag, seal bag, and refrigerate for at least 1 hour or up to 24 hours.

When ready to finish cooking chowder, drain whole clams in fine-mesh strainer set over bowl; reserve juice (you should have about 1 cup; add water if necessary to make up difference).

Combine potato mixture, reserved clam juice, and remaining 1½ teaspoons salt in large saucepan. Bring to bare simmer over medium heat (bubbles should just begin to form along edge of saucepan), stirring often (it will take about 10 minutes to reach bare simmer). Reduce heat to medium-low and cook, stirring often and adjusting heat to keep chowder just below simmer, until potatoes are mostly tender, about 5 minutes.

Stir in whole clams and cream. Increase heat to medium and cook, stirring often to keep chowder just below simmer, until potatoes are fully tender and chowder is hot throughout, about 5 minutes. Off heat, stir in butter and potato flakes, if using, until combined. Season with salt and pepper to taste. Serve with oyster crackers.