First Fastboot is an application that is available from the Android SDK. It is a separate application ran on your computer to communicate with your device thru the bootloader.
I think the question your probably asking is if you should leave your bootloader locked or unlocked. If it is already unlocked, leave it. You can always lock it back up in the event you need to have your device serviced or sold. I say this because normally on most devices when you unlock the bootloader it wipes the device, so if its already unlocked then just leave it. My opinion.