I have mantis 4.3.0 running on a gen1 iPod touch. I've not upgraded to fw3 yet, but am having problems with the app:
1. The app crashes to home screen if I select notes, or search
2. I cannot select different bibles, they appear with a questionmark next to them and the app crashes if I select one of them
3. I cannot see any of my notes online
4. The app crashes if I select history from the Reading view
5. The app crashes if I select bookmarks from the Reading view

I am worried that all my notes have been lost. What can I do?

If you have backed up your notes, they are not lost.

You can try to restore back to 4.2.0 from an iTunes backup, or you can try upgrading to iPhone OS 3.1.

We have put a fix in with Apple and are waiting for them to approve it. This new version will work with OS 3.0 or above (but not 2.x or lower.)

So, the app has failed, and lost my notes? Is the backup something I have to do manually or is it automatic?
If manual, how do I configure it?
I'm confused about the solution. Is the previous backup the only way to get the notes back, or will upgrading to 3.1 do it for me?

You backup manually using the Backup button at the top of the Notes screen. Alternatively, if you have backed up your iPhone from iTunes you could restore the app and your notes from iTunes as well.