Make the secret sauce: Stir together mayonnaise, ketchup, relish, mustard, vinegar, salt, and pepper in a small bowl. Cover and refrigerate until ready to serve.
Caramelize the onions: Heat canola oil in a small skillet over medium heat. Add the onions and cook until softened, about 6-8 minutes. Reduce heat to low and continue to caramelize until deep golden brown, about 30-40 minutes. Remove from heat and set aside.
Prepare the fries: Cook the frozen fries following the package directions.
Melt the cheese: Preheat broiler with the oven's top rack positioned 2-3 inches from the upper heating element. Arrange the cooked fries on a baking sheet and top with the cheese slices. Broil until the cheese is melted, about 1-2 minutes.
Assemble with toppings: Remove the cheesy fries from the oven and top with the caramelized onions and secret sauce. Serve immediately.
