Sorry for the delayed response...
The short answer is, as long as the iOS app is connected to the amp, the "eq" settings will be sent when you switch channels.
The longer answer is that as long as you are working with a saved setting file (i.e. you have loaded a previously saved setting file, or you have saved your current settings to a file), the "eq" settings will be sent when you switch channels.
When the app is first loaded (and no settings file has been loaded ort saved) settings will not be setn to the amp when the channel changes. This is to prevent unintentional stomping of amp settings.
Hope that helps.