I arrange my chests so that when I shift-click items into it, they fill the slots I've designated for the items. So there is one item in each slot that I'd like to fill, so I don't have to organize later. I always keep one in the chest.
I currently have a chute for food items produced by my farm that feeds into an already organized chest, but the items will not go into the incomplete stacks in the same way as when I Shift-click items in.
The Hopper will however complete stacks that it has started itself. As soon as I interact with that stack or move it, it will not fill it, and will place the item in the next open spot in the inventory.