To ensure that you have a good safe copy of your iWeb site, you only need to back up one file, (which should be done as part of your regular data backup). This file is your domain file, and it lives here:
User/Library/Application Suuport/iWeb/Domain.sites
When I say back up, I mean that you should copy either using backup software or not your data files from your Mac to an external source. Whether it be CD, DVD, iDisk, External Hard Drive, USB Drive, many possibilities. The reason that I suggest using an external source is twofold.
Firstly, if you Mac is stolen or severely damaged, you have all of your data elsewhere.
Secondly, if you just back up to your Macs Hard Drive and this drive become corrupted, then you may not be able to access your backup.