What you might want to do is create different iWeb content files for each project. There is normally one file in your personal "Application Support/iWeb" folder called Domain.sites2. iWeb is suppose to allow you to double click on any one of those file types to open and edit them. Backup before you try this idea.
How I would test this is to create a project folder in my home directory. Copy the Domain.sites2 file to the project folder. Make as many copies of it as I have sites. Strip the sites down to one for each file. Then you should be good to go.
iWeb is also suppose to remember the last file you opened and will open that one when you start iWeb.
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