In pot one, saute onion, celery and bacon in the oil over medium heat for 5 minutes. Add ½ of the potatoes, celery, thyme, salt & pepper, and red pepper flake. Just cover the veggies with stock, keeping the remaining stock for the other pot. Bring to a simmer, covered for 10 minutes until potatoes are tender.
While pot one is simmering, add the rest of the potatoes and stock to a smaller pot. Bring to a rapid boil for 10-12 minutes until potatoes are tender. Then puree by immersion hand blender or by putting in a blender until smooth. If you use a blender, cover the lid with a hand towel and hold tight. The pressure could spit the lid off. Yikes.
Remove bay leaves and thyme sticks, leaving the leaves in the soup. Add pureed potatoes, milk and clams (with liquid) to pot one. Stir, taste, re-season with salt & pepper, and serve.