I think you're getting way ahead of yourself here! The US State Dept has no chance of holding any sway over the Italian judiciary (e.g. the choice of appeal judge), and nor - I suspect - would it want to be seen even attempting such a thing. The US Govt might hold some subliminal sway over the Italian executive branch of government, but the Italian executive has no sway over the judiciary either (and nor should it) - as Berlusconi is currently finding out!
I don't think the State Dept has been doing any more than keeping an eye on this case. It's an ordinary criminal case in a sovereign nation which is a US ally, but a case which just happens to involve a US citizen as a defendant. Personally, I suspect that even if Knox gets ultimately convicted (which I think is moot because I think she'll be acquitted in this appeal), there will be no "behind the scenes" moves from any branch of the US Government: Italy should be allowed to manage its criminal justice system as it wishes, so long as there are no fundamental breaches of human rights.
That's why I think that the pro-guilt groupthinkers who continue to crow that "the State Dept thinks there is nothing wrong with this case" are on totally the wrong track. The US Government would never say anything else - certainly not in public, and almost certainly not in private on-the-record conversations either. The standard practice for countries whose citizens are on trial for offences committed abroad is for the local embassy or consulate to send representatives to
a) meet with the suspect, to ensure that (s)he has adequate legal representation and is being treated properly,
b) ensure that the defendant's family is kept in communication if required,
c) monitor the trial to ensure that the proper judicial procedures are performed.
It is diplomatically out of order for anything more than this to occur. Even if officials within the US State Dept perceive that a miscarriage of justice has taken place regarding US citizen Amanda Knox, it will still fall well short of communicating that concern to the Italians or anybody else. That's the way that international diplomacy works - particularly with countries that are reasonably important military and trade allies.