You need to publish your iWeb website to a folder first. Since publishing to a folder in iWeb changed from iWeb '08 to iWeb '09, check with the iWeb manual for the correct way to publish a website to a folder. The iWeb manual is located under the Help menu in your menu bar when using iWeb.
Apple provides a video tutorial on publishing your site with iWeb '09. In iWeb '08, just go to the File menu and select 'Publish to folder'.
Once you have done this simply open your published site in iWeb SEO Tool. You can use iWeb SEO Tool's built in publishing features to publish your site to MobileMe or to your FTP server once you have added all your website tags.
Warning: Do not use your iWeb domain file. This is not the correct file to use in order to optimize your website.
You can also view the following video tutorial which will show you how to load your website in iWeb SEO Tool (if you publish to FTP)
http://www.ragesw.com/blog/2011/02/26/how-to-load-your-site-in-iweb-seo-tool-ftp-users/