Unfortunately, at least in this first iteration, the "Search iPhone" feature only searches the iPhone's built-in databases: there's no way for third parties to make their own data available to be searched.
We're hoping this changes in the future: we've designed OmniFocus to be able to provide that data to them easily, and we've sent feedback to Apple asking for search to include results from third-party apps. If you also
send feedback to Apple, presumably that will make it even more likely that it will be included in a future iPhone update.