I cannot explain this concept well in words. I thought that addItem() was adding instances to the stage (as in the root, or as3 stage). However it appears when you enter edit mode on an item then mainFla.addItem(), that edited item gets the instance.
mainFlaLibrary.editItem("Face");
selectedIndex = mainFlaLibrary.findItemIndex("Eyes");
selectedItem = mainFlaLibrary.items[selectedIndex];
mainFla.addItem({x:0, y:0}, selectedItem);
This is equivalent to double clicking the Face, and dragging an instance of Eyes into it from the library.