It really all depends what type of app data you're storing. If you need to recreate java objects exactly how they were (i.e. variables and state the same), you can serialize the objects you need. There are many serialization mechanisms, for example, xstream as you mentioned. If you're storing objects directly, using one of those mechanisms would work.
But, a lot of times, you want to store the state of your application, which doesn't necessarily correspond directly to serializing objects directly. If that's the case, you can write out only the relevant data you need. The type of storage you use depends on your needs. If you have a large amount of data, consider a database. A smaller amount might work better in a flat file.
One other thing is that storing data redundantly in a single file doesn't seem too useful. If the file gets corrupted, you'll lose both copies, so if redundancy is a concern, store it in different places (i.e. a primary and backup database).
There's no one right way to do it, but hopefully these ideas get you started.