'Stuffing' is used when you force a large amount of soft bulky material into a bag or cavity, usually in order for it to retain its shape. Stuffing is used in armchairs, pillows, cushions, and animals (both toy ones such as teddy bears and real ones such as turkeys ready for the oven). 'Filling' is more general. A filling can be of any consistency and doesn't determine the shape of the object. For example, a filling in a sandwich is simply whatever you choose to put between two slices of bread - it might just be a slice of cheese or meat. A filling in a donut might just be a spoonful of jam.