Preheat your oven to 400℉. Spread the bread cubes on a baking sheet and toss them with 1 tbs olive oil, sugar, and cinnamon. Bake the cubes until golden and crunchy, 10 to 12 minutes. Remove from the oven and let the croutons cool on the baking sheet. Try not to eat too many as you make the soup.
Heat a large soup pot or Dutch oven over medium heat. Add the remaining 2 tbs olive oil and butter. Add the onions along with a pinch of salt. Cook until softened, stirring often, then add the garlic and cook, stirring, for 30 more seconds. Pour in the amaretto and cook about 5 minutes, stirring and deglazing.
Add the squash and stock. Cover, reduce the heat to medium-low, and simmer until the squash is soft. This will take roughly 20 minutes, but possibly faster. Once the squash is soft, remove the pot from the heat and use an immersion blender to puree the soup until very smooth. Put the pot back over low heat and stir in the cream. Add more salt to taste, plus black pepper.
Ladle the soup into bowls and garnish with plenty of croutons, scallions, and chopped pecans.