As of iAnnotate 4.0.1 you can add files and folders to iAnnotate via iTunes File Sharing. To do so, first add iTunes File Sharing as a location in your Library. Tap the "+" -> Add Storage -> iTunes File Sharing
Once that is done, you'll see the new location in your library:
To add files in iTunes, connect your iPad to your computer. Click the iPad icon in the upper left corner of iTunes.
Click Apps on the left, then scroll down to File Sharing and click iAnnotate.
Documents added here will show up in the app and vice versa.