USB is not bootable, so you won't want to use Carbon Copy Cloner to backup your iBook. (You won't have a process of getting it back off the USB hard drive and onto your iBook if you needed to.)
I think partitioning the USB hard drive into two 40GB drives is a good idea. This way you can have one drive with your full backup and the other for other files.
If you've already partitioned your USB hard drive, you can put your Mac OS X install disk into the iBook's drive, restart and hold down on the "c" key. This will startup the iBook from the install disk. You will be asked to choose a language, but don't continue with the installer past the next screen. Instead, choose to open the Disk Utility form the Utilities menu. In the Disk Utility, select the name of your hard drive on the left-hand side (probably "Macintosh HD") and then select the "Restore" tab on the right-hand side. Drag the icon of your "Macintosh HD" to the "Source" field and then drag the name of your backup hard drive to the "Destination" field. If you select the option to "Erase Destination" (which should be fine), the Disk Utility will move blocks of data rather than individual files and it should copy faster. When you're done, you can quit the Disk Utility and then quit the Installer to restart back to your iBook's hard drive.
This process won't allow you to do an incremental backup (only backing up files that have changed since the last backup), you'll have to do a complete backup each time. But, you can use the install disk to "restore" the other direction back to your iBook's hard drive if you ever needed to.
I've never actually made a backup to a USB drive, I've always used FireWire. It's possible, that since USB is not bootable, if you "restore" your backup back to your iBook, you might not be able to boot from it. That's something I would have to experiment with to find out for certain. But, maybe someone else could verify that doing a restore from a USB drive is still bootable.
-Doug