RE:Flex will deal with the Alpha Channel correctly but you should maybe merge the face layers you want to warp in one comp. In AE I think you need to explicitely use Import as opposed to DragAndDrop to get the Layer Options from a PSD. You might want to take the resulting comp (from importing as layers), duplicate it, go in comp1, turn off all that is not eyes,mouth… then drop comp1 into comp2, and apply RE:Flex over comp1. Then you can use Composition | Save Frame As :: PSD and it will reexport one layer per layer in your comp. If you really want to warp things separately then you need to make each layer separately (with their own alpha channel then). If you do so then you might end up with small holes (or if you make an eye smaller by itself, then still have the other eye under it once merged), we have RE:Fill to help for that problem 🙂
Pierre
http://www.revisionfx.com