You can indeed have mulitple .htaccess files across a site, but only one in a directory.
And here is my .htaccess file for my wp install:
RewriteEngine On
RewriteBase /T2/
RewriteRule ^archives/category/(.*)/(feed|rdf|rss|rss2|atom)/?$ /T2/wp-feed.php?category_name=$1&feed=$2 [QSA]
RewriteRule ^archives/category/?(.*) /T2/index.php?category_name=$1 [QSA]
RewriteRule ^archives/author/(.*)/(feed|rdf|rss|rss2|atom)/?$ /T2/wp-feed.php?author_name=$1&feed=$2 [QSA]
RewriteRule ^archives/author/?(.*) /T2/index.php?author_name=$1 [QSA]
RewriteRule ^archives/([0-9]{4})?/?([0-9]{1,2})?/?([0-9]{1,2})?/?([_0-9a-z-]+)?/?([0-9]+)?/?$ /T2/index.php?year=$1&monthnum=$2&day=$3&name=$4&page=$5 [QSA]
RewriteRule ^archives/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([_0-9a-z-]+)/(feed|rdf|rss|rss2|atom)/?$ /T2/wp-feed.php?year=$1&monthnum=$2&day=$3&name=$4&feed=$5 [QSA]
RewriteRule ^archives/([0-9]{4})/([0-9]{1,2})/([0-9]{1,2})/([_0-9a-z-]+)/trackback/?$ /T2/wp-trackback.php?year=$1&monthnum=$2&day=$3&name=$4 [QSA]
RewriteRule ^feed/?([_0-9a-z-]+)?/?$ /T2/wp-feed.php?feed=$1 [QSA]
RewriteRule ^comments/feed/?([_0-9a-z-]+)?/?$ /T2/wp-feed.php?feed=$1&withcomments=1 [QSA]
RewriteRule ^stats/author/(.*)?/page/?(.*)?/?$ /T2/index.php?wp_stats=1&author=$1&page=$2 [QSA]
RewriteRule ^stats/author/?(.*) /T2/index.php?wp_stats=1&author=$1 [QSA]
RewriteRule ^stats/ /T2/index.php?wp_stats=1 [QSA]
RewriteRule ^stats /T2/index.php?wp_stats=1 [QSA]
RewriteRule ^recent-links/feed?/?$ wp-recent-links-rss2.php [QSA]
RewriteRule ^recent-links?/?$ wp-recent-links.php [QSA]
RewriteRule ^recent-links/([0-9]{4})?/?([0-9]{1,2})?/?$ wp-recent-links.php?y=$1&m=$2 [QSA]
I have no idea *how* it works, but it does.
The top lines concerning archives were generated by the permalinks part of wordpress.
Everything following that is an addition for a plugin to correctly function.