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a) File-Backup Wallet
This will just make a copy of the wallet.dat file in a location you specify.
b) Encrypt Wallet
This will encrypt the private keys that are in your wallet.dat with the supplied password. Any function that requires a private key (such as spending bitcoins) will require you to re-enter the password.
2. should the whole Bitcoin-Qt application be placed in an TrueCrypt encrypted drive or just the wallet.dat file should be placed in this encrypted drive?
That depends on what you are trying to accomplish. Are you trying to hide the fact that you are running a bitcoin wallet, or are you just trying to hide your bitcoin addresses?
3. is there a manual of Bitcoin-Qt for non-geeks available?
Not that I'm aware of, but you'll find many answers by searching these forums and are welcome to ask questions here as well.