Let's say you have a stack of buckets. You go to milk the cow and the stack of buckets becomes a stack of milk. It doesn't go separate a stack of empty buckets and a stack of milk buckets, it makes the whole stack of empty buckets a whole stack of milk buckets. For example, I crafted 4 buckets, I go to get some milk from an cow, I click once and my 4 buckets become 4 milks in one go. Not one milk and three empty buckets, just 4 milks.