Hi,
There is a number of ready backup solutions for Mac (I assume you are on a Mac judging by your signature) including Apple Time Machine that ships with Mac OS X. I prefer SuperDuper! -
http://www.shirt-pocket.com/SuperDuper/ ... ption.html
SuperDuper! can store full bootable HDD backups, as well as smart update backups that only store what's been updated since last backup. So here's my way to configure backup using SuperDuper!:
First create a full bootable HDD backup onto external USB drive. It will format the external drive and copy your entire system drive image to external drive and will make it bootable - it becomes a perfect clone of your system drive. Then configure a customized "smart update" backup schedule to run at the specified time of day of week. You may also choose specific folders for it, as it defaults to the entire disk. This is it. Next time the schedule is run, the smart update will check what has changed since the last backup and will transfer the new and updated files to the backup drive.
On my system "smart update" is seamlessly performed every night and my external drive is always attached to my computer, which is on all the time as well. I am pretty happy with this solution as it is transparent and basically lets me to forget about backups, until they are needed.
SuperDuper! is not free but it's excellent for my needs. As a free alternative, you may look into Carbon Copy Cloner (CCC).
Hope it helps,
Andrejs