WP permalinks broken

No big surprise that I’ve hit this given it seems to be one of the most common problems WP users encounter. I’ve been trying to connect with the iPhone WordPress app and have not been succeeding. I still haven’t gotten around that, but I did notice that besides the main page, links were not working on the blog.
I’d changed to a non-default permalink option. And that was causing 404′s. It seems to be that when I do this WP was supposed to automagically update an .htaccess file for me, but this isn’t happening. Changing back to the default permalink style and sub-pages on the blog are working now.
Still no forward progress on the iPhone app connection hanging.
Between looking at the .htaccess and the Fedora wordpress-mu.conf for apache, it’s also clear to me that I’m not currently understanding how the site is supposed to work in general. I need a server work flow diagram or something that shows when a request comes in how it hits apache, what rules do/might apply, how it then hits which WordPress scripts, how those then pull up different content from the filesystem and database and direct to other URLs and any subsequent apache involvement around redirecting. There’s multiple pieces here, their interaction’s design isn’t clearly spelled out and involves a bit of magic, and I’m not a standard install. Plenty of places for subtle configuration breakage.
And configuration breakage is where I am.