The "best" way is whatever works best for you and your situation. As you probably know, there are a billion-and-a-half different backup programs in existence. If there was one, single, "best" way, this wouldn't be the case. Different backup strategies work for different people in different situations.
Do you want compressed backups? Bootable backups? Incremental backups?
You may want to have a look at Chronosync (available with a simple Google search). It can be scheduled and has options to perform different kinds of backups and syncs.
If you can describe your situation and needs in greater detail, we may be able to narrow down your options to something that will work "best" for you.