Preheat the oven to 400˚ F. Line a baking sheet with parchment paper. Combine 5 tablespoons olive oil, the onion, leeks, 2 teaspoons thyme, a big pinch of salt and a few grinds of pepper in a large pot or Dutch oven. Cook over medium-high heat, stirring occasionally, until the onion is tender, about 10 minutes. Add the sweet potatoes, parsnips, chicken broth, 3 cups water, 1 teaspoon salt and the cayenne. Bring to a boil, then reduce the heat and simmer until the potatoes and parsnips are tender, 12 to 15 minutes.
Meanwhile, cook the bacon in a small skillet over medium heat, stirring, until browned and crisp, 5 to 7 minutes. Transfer the bacon and drippings to a large bowl.
Add the bread, cheese and remaining 1 tablespoon olive oil to the bacon and drippings. Season with salt and pepper and toss, then spread out on the prepared baking sheet. Bake, tossing once or twice, until toasted and the cheese is melted, 10 to 12 minutes.
Meanwhile, puree the soup with an immersion blender until smooth (or puree in batches in a regular blender). Season with salt and more cayenne to taste. Thin with water as needed. Divide the soup among bowls. Top with a swirl of creme fraiche, the croutons and the remaining 2 teaspoons thyme.