It is not a general expression. It is a funny way of saying that someone knows nothing about the particular thing in question (here the act of preparing food from the pig), and indicating that they wouldn't really know where to start with the task. It is likely to be used where actually it would be very easy for anyone to at least work out which end was which. "Do you play the guitar" "No, I don't even know which end is which" "We need an extra player for the weekend, can your friend Barry play tennis?" "I'm not sure he knows which end of the racquet is which"

Someone who may not know which end of the pig is which, just means someone who is stupid, or doesn't (in this case) know much about food.