You can do many things with the backup NAND.bin.
1. You can create an EmuNAND partition with it. This is useful if you, for instance, downgrade to 4.5 and want to use EmuNAND with your backup.
2. You can restore your SysNAND using your NAND.bin, by going into the Gateway menu, by holding up when going to the downgrade menu. This is useful when you format your SysNAND, or downgrade / upgrade and want to get it back.
DO NOT delete your NAND.bin. If you completely mess up your console by bricking it, you won't be able to ever get it back to normal, and you might as well throw it away. At least if you have the backup, you'll be able to do a hard-mod and get your stuff back.