i would also like to point out that the tsuku chain and amaterasu have their effects programmed intovthe system so if your opponent is doing their skills manually they are either cheating or wasting effort
Actually Ama machinic doesn't work while it's in legion (well last update it didn't I'm not sure if they implemented it this update since I haven't had time to cardfight) so you had to use it manually.
I think it only tells you when it goes on the top of the deck. Since when I put it to the bottom it never saids it went to the bottom.
Spoiler
(http://i1129.photobucket.com/albums/m511/TSSorSGD/AreaHelpTopBottomDeck.png)