Hm, I’ve tried it in the root directory, the wordpress directory, and now in both directories.
permalinks only work when .htaccess is in the root directory and in both directories. However, wordpress won’t automatically update .htaccess regardless (even with permissions set to 666 for both files).
I may just have to be stuck with manually updating .htaccess when I add pages.
Another possible clue:
under Manage–>files
it thinks that .htaccess and the main template (index.php) don’t exist.
They clearly do, they are visible by ftp, shell, and most of all the website works.
Sorry I had read another post that said it should be where your index.php is.
But, I tried putting this in my wordpress install directory. wordpress still doesn’t automatically update .htacess