This is just me (and I mainly did it this way because I built my blogs over time) but I have my blogs setup individually, I use the cPanel install tool to make it faster then just add a standard set of plugins.
I then use Windows Live Writer to manage all my blogs from one place. There are quite a few Desktop Blog Managers about though. It does make it a hell of a lot easier then loging in to each one for updates.
I am sure there are better ways then this, but this is just what I do.
Edit: This also allows me to use different hosts and IPs etc. I am not sure if the Mapping Plugin would do that.
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