I haven't used .Mac since before iWeb so I'm going to have to assume based on your e-mail that even if you have a site name hi-lighted, that iWeb uploads all of the site projects.
If my statement above is true, then probably the only way around this is to create a special iWeb project file just for content you want posted to .Mac.
You'll find a Domains.sites file your "Library/Application Support/iWeb" folder. According to Apple online notes, you can have more than one of those. The problem is you have to manually click on the one you want opened because iWeb only opens the one it was last editing.
Anyway, you could copy the current Domains file, double click it, remove the stuff you do not want on .Mac, and then upload. That is the theory.