Hello, it is tough, I know...but all your questions are valid, so let me try to clarify to you...
File Vault (2) will encrypt your entire disk, including the user folder, so if all your files are already encrypted then it does not make much sense to encrypt some folder once again.
Whereas File Vault seems to be working fine and Apple continues to use it in OS X, there is always this "what if something goes wrong" and due to some bug in File Vault or error on disk, you loose it all? If the drive is encrypted then no recovery software can help you, it is either all or nothing.
The alternative is to protect only some folders and leave the rest unencrypted, yet, this assumes that you will protect your most valuable data which brings the very same question up again, "what if....", yes, you would not loose the entire disk, just your most valuable data :-)
So I guess the choice is yours, all I can say is that in several years since I support this product, there was no report on data corruption unless it was a corruption of the disk itself. If you add to it the possibility (and recommendation) to backup those disk images, then the whole thing is quite safe, in worst case we could restore an older copy of the disk image containing the data.
The data on the backup disk is saved in the encrypted form, so it is protected in the same way as on your startup disk, no worries here.
Now to the application protection, Espionage 2 offered an "no brainer" application protection, you would pick the app you want to protect and we would to it all automatically for you.
Due to tightened security in OS X, we had to change the way Espionage works, and this does not allow us to intercept application launch any more, so we had to give up on application protection all together. However, the application protection is nothing else then protection of specific folders where application stores it's data, so "if you know what you are doing" you can still do it, but in our tests with Apple's Mail, whereas it works and does what is expected, due to the way IMAP and Apple Mail work, if you lock the folders, Mail will simply download the messages from the server again, we cannot prevent this, as we cannot prevent it from accessing your mail account info. What would be protected are the local folders: if you move some mails from server into a local folder, then the local copy is the only one, and this could not be fetched again, and this would not show up if the Mail folders are locked.
So if you have a specific Mail workflow, then it is worth the trouble.
I hope I made it clear(er) to you, if you have any further questions, let me know
Zsolt