forget the D2D download, go directly over to Eagle Dynamics, download it from there. the download from there is for free, you can start right now, you only need to buy the activation key. I think on D2D, you have to buy the game before you can download it. I'm not sure if you can activate the downloaded game with the key from the boxed version, but I really don't see the reason why not.
the manual is just printed version of the .pdf version that can be found in files, only in color and nicely bound