The only thing you need to use the App Store for is ForeFlight updates. In-app purchase (used for subscriptions) is initiated from within ForeFlight. All of the various downloads are handled within ForeFlight as well.
What kind of issues are you having with plates?
Some parts of ForeFlight, such as Imagery, the street map, and weather data need to be retrieved from the internet (or XM via the Baron link if you have it). If you're in flight and you don't have XM or Internet access, there's no way for any device or app to display live weather.