publishing one site to a folder?
Couldn't you just move your Domain.sites2 to some other location and then open up iweb? i moved mine to my documents folder. now when i want to work on it i just navigate to it, double click and voila. after you have moved that file, iweb will open as it would if you did not have any sites at all. this gives you the chance to start a new site and will also create another Domain.sites2 file. however, please note that you don't want to organize both Domain.sites2 files in the same place. this will cause iweb to seriously wig out and you probably will lose all your work b/c the program will get confused. you should be able to publish each site one a time this way.
hope this helps and isnt too confusing.