When you say App, I'm assuming you mean the version of FTM 3 that comes from the app store compared to the version you download from the website. Is this correct?
The apps for your ipad or iphone are just for ancestry. They aren't related to FTM except if you change your online tree via the app, you will need to do a sync in FTM (if you have your trees synced).
From reading the message boards, the version you download from the website (NOT the app store) is better because you get the updates faster. If there's an update to FTM 3, the app store version has been taking a few weeks longer to get the updates.
The other nice thing about the 6 month membership, is, if you already subscribe, you can call customer service and just have the 6 months added to your account.