I have run small businesses but not yet bakeries specifically.
- you can't restock sold items. You need to actually bake them again and again. You can hire personel and order them to bake for you
- there is a food display in the game that keeps baked goods longer fresh. There is one in businesses and hobbies, a second one was in the early buyers items. The food displays from get to work should work as well in a small business. (personally I like to use the fresh chef reward trait but that's a lot of work to acquire if you don't want to cheat.)
- You have to set activities for your bakery. You can just tell your customers to just buy goods but you could also add eating if you want to. Or start selling coffee and tea to customers. Whatever type of bakery you want.