So in the DF Wiki on the Workshops page it mentions to "Remember to turn off prepared food." on the stockpiles.....why exactly do we do that? Is this so the prepared food isn't broken down to be used again? or just in general it's a bad practice to store prepared food?
There is no reason why you can't store prepared food and their ingredients in the same stockpile. But "food"->"prepared food" is a production chain of raw material and processed material. Whenever you have a production chain, you usually want to separate the stockpiles for raw materials from those for processed materials.
- In order to minimize walking distances of your skilled laborers, you want each material closest to the place where it is consumed. That means you want the ingredient stockpile to be next to the kitchen and the prepared food stockpile next to the dining room tables. When you do this, then it is no longer that important to keep the kitchen close to both farms and dining rooms. Transporting goods to a stockpile is "Hauling" labor, so your most skilled dwarfs don't need to waste their precious time on food logistics.
- Having separate stockpiles for each step of a production chain allows you to see at first glance how much raw materials and processed goods you have. With a mixed stockpile, you might have to enter "Look" mode and examine the individual tiles of the stockpile to find out what's actually in it.
- When you use the same stockpile for two stages of a production chain, then that stockpile might get filled completely with raw materials leaving no room for the product. That means if your combined stockpile gets completely filled with ingredients (which happens very easily when it's harvest time and you are short on barrels), then the prepared food stays in the kitchens, which slows down the cooks and prevents them from processing that huge stack of ingredients efficiently.
The reason why the wiki mentions processed food specifically is because the stockpile user interface has a weird inconsistency in this regard. Usually you use the three-tiered category list to specify what belongs into each stockpile, but for processed food you toggle them on and off with u while you are in the "Food" supercategory. If you forget to pay attention to this toggle, you might find stacks of prepared food mixed up with the plump helmet seed bags near your farm plots or with your pig tail barrels next to your clothes industry.
You usually want to have a separate stockpile for storing prepared food and drink that's next to your dining area.