This is cut from a quick and dirty email that I wrote to someone. It may not be well organized or explained, but I thought it was better posted here than nowhere at all.
Ok so the trick that I use is to use the multiple site feature of drupal to make upgrades easier. I use several symbolic links on the file system to make it all work let me describe it here.
My hosting company allows me to host multiple domains on the same account. by default the addon domains document roots are sub folders of my main domain's document root. for example it's like this:
~/public_html