I would like to run multiple boards on one web site, each with an entirely different set of forums and members. Is it possible to share the basic files between multiple boards to make updating simpler, or does each board have to be completely independent.
Not entirely what you want but you can use the same installation by setting up sub-forums. Each sub forum can have it's own style to distinguish it from the others which would make it appear to be separate. If you need to restrict access you can set up usergroups for each sub forum. Instead of having to register for separate forums they could instead register once and request permission to join the usergroup.
“Results! Why, man, I have gotten a lot of results! I have found several thousand things that won’t work.”
use htaccess to get a bored id like http://www.yoursite.com/_community/3/ would be forum 3, in the config file do like if ($_GET[forum_id]) { sql info for forum 3 }