Is there an advantage in synchronizing my iPod manually?

Choosing "Automatically sync when this iPhone/iPod is connected" is the most convenient option, as long as everything is going the way you want. This option ensures that any change in your iTunes library will be replicated to your iPhone or iPod when you connect it with your iTunes library.

But, if the contents of your iTunes library were damaged or deleted for some reason (e.g. iTunes reinstall, re-installation of your operating system or break down of your hard drive), the automatic update may pose a risk. By synchronizing your iPod or iPhone with a damaged or deleted iTunes library you risk to erase the entire contents of your iPhone/iPod. In case of a problem or if you doubt about the contents of your iTunes library, make sure you choose the "manually manage music and videos" mode to prevent data loss.

Where to set up the “manual iPod management”?
Open iTunes and connect your iPod/iPhone. Choose your device in the left column and select the first tab called “Summary”. Now check the option “Manually manage music and videos” and confirm with “Apply”. You are now managing your iPhone or iPod contents manually and don’t risk to automatically synchronize your iPod and iPhone with an empty iTunes library.