Bring the half-and-half as close to room temperature as possible before adding to the chowder to help keep it from breaking.
Combine potato mixture and 1 1/4 cups water in a microwave-safe measuring cup. Microwave at HIGH 8 minutes or until potatoes are tender. Set aside.
While potatoes cook, combine remaining 1 cup water, clams, thyme sprigs, and bay leaf in a Dutch oven; bring to a boil over medium-high heat. Cover, reduce heat, and simmer 6 minutes or until shells open. Remove clams from pan using a slotted spoon, and discard any unopened shells. Strain the cooking liquid through a fine mesh sieve over a bowl; discard solids. Cool clams slightly. Remove meat from shells, and chop. Discard shells.
Heat a medium saucepan over medium heat. Add bacon to pan, and cook for 4 minutes or until browned and crisp, stirring occasionally. Remove bacon from pan using a slotted spoon. Increase heat to medium-high. Add the celery to drippings in pan; sauté 3 minutes or until tender, stirring occasionally.
Combine flour and bottled clam juice in a small bowl, stirring with a whisk until smooth. Add clam juice mixture and reserved cooking liquid to pan. Bring mixture to a boil; cook 1 minute, stirring constantly with a whisk. Add reserved potato mixture and chopped thyme to pan; reduce heat, and simmer for 5 minutes, stirring occasionally. Remove from heat. Stir in chopped clams, half-and-half, and salt. Divide chowder evenly among 4 bowls; sprinkle evenly with bacon, pepper, and chives. Serve with crackers.