The iTunes update will likely be located in software update. Or you can go into the iTunes menu itself and "Check for Updates".
If you're updating the iPhone, the typical procedure has been to dock it and there will be a button in iTunes to "check for updates" for the phone. You can then download that and install. If you're getting a new iPhone, it will already have the 2.0 software.
The app store, i believe, will be both in iTunes and the new iPhone 2.0 firmware. Download times are subject to your internet speed.