Preheat the oven to 350 degrees F. Lightly grease a 9x13 inch casserole dish.
Heat a large skillet over medium-high heat. Add 1 tablespoon butter. Once melted, add the yellow squash and yellow onion. Sprinkle with ¼ teaspoon salt. Saute for 8-10 minutes, or until the squash and onion are softened. Stir occasionally with a spatula to evenly cook.
While the squash is cooking, prepare the cream sauce. Heat a large skillet (it should be able to hold at least 2.5 cups of liquid) over medium-high heat. Add ¼ cup olive oil. Once hot, sprinkle in the minced garlic, chopped thyme and oregano. Saute about one minute, until garlic is golden.
Sprinkle ¼ cup all-purpose flour into the garlic. Cook another minute until the flour is lightly browned, stirring frequently to prevent burning. Slowly whisk in ¼ cup coconut milk to form a thick paste. Slowly pour in remaining milk, whisking consistently to prevent lumps from forming. Sprinkle in ½ teaspoon salt, nutritional yeast, paprika and cayenne pepper.
Bring to a rapid simmer over medium-high heat. Reduce heat to medium-low and simmer until thickened enough to coat the back of a metal spoon without sliding off.
Crush one cup of crackers into small pieces. In a small bowl, mix together the crushed crackers and 3 tablespoons melted butter. Set aside.
Assemble the casserole in the lightly oiled 9x13 baking dish. Start by evenly layering the onions and squash (make sure to drain off any excess cooking liquid before adding the squash). Pour the cream sauce on the squash. Sprinkle freshly ground black pepper liberally across the top of the cream sauce. Evenly spread the crushed crackers across the casserole. Sprinkle with shredded vegan cheese (optional).
Cover with foil. Cook at 350 degrees for 15 minutes. Remove the foil and cook for another 10 minutes, or until the crackers are golden. Remove from the oven and let rest for 5 minutes before serving.
Herbs: One tablespoon fresh chopped herbs can be replaced with one teaspoon dry herbs.
Flour: All purpose flour can be replaced with a gluten free all-purpose flour blend to make this recipe gluten-free. Choose a gluten-free cracker or omit entirely.
Coconut milk: Choose unsweetened and unflavored "coconut milk beverage" that is found in cartons, not canned coconut milk. Soy or almond milk can be used in place of coconut milk.