I think that you may be able to publish more than one site in iWeb '09. However, after experiencing the same as you with an earlier version of iWeb, I've come to rely on a program called iWebSites. It is a donationware program that you can download from Mac OS X Software Updates and Mac OS X Downloads - VersionTracker
or from MacUpdate: Download Apple Mac Software & iPhone Software
I know that I sent a $5 donation and should do so again as I have come to rely on this program.
In my Sites folder I set up an iWeb Sites folder. Whenever I work on an iWeb site it gets saved to the iWeb Sites folder. Sometimes it can get confusing and you will decide to save to User/Sites/iWeb Sites/sitename folder. When you do this, you end up with the latest version of the site inside the sitename folder. I've learned to choose the iWeb Sites folder to avoid multiple folders of the same site. Your different sites will appear in the iWeb Sites folder.
Whenever you want to work on a site, launch iWebSites first, choose the site you want to open. Sometimes you have to try more than once. If the wrong site open, Quit iWeb, go back to iWebSites and choose the site you want again.
When backing up, I usually save a copy of my iWeb Sites folder and I also go to User/Library/Application Support/iWebSites/sitenames.xml I save a copy of the iWebSites folder containing the sitenames.xml file. I usually keep these backups on a flash drive or an external HD
Hope that helps solve your problem. Been there, done that.