How do I use .htaccess to trigger mod_rewrites before D7's Clean URLs take over?
Personally, I would see if the Redirect module works for your needs.  Is it basically a UI interface for making 301 redirects.  Off the top of my head, though, I don't recall if it will work with patterns.

If that doesn't work, then your best bet is to put them in the .htaccess right after the 

# RewriteBase /


line.

Just remember that mod_rewrite will continue to process rules unless you use the L flag.  You also want to explicitly give the response code with the R flag.  Something like this should work

# RewriteBase /

RewriteRule ^some/path/(.*) /other/place/$1 [R=301,L]
RewriteRule ^another/hierarchy/(.*) /different/thing/$1 [R=301,L]

# Pass all requests not referring directly to files in the filesystem to
# index.php. Clean URLs are handled in drupal_environment_initialize().
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteCond %{REQUEST_URI} !=/favicon.ico
RewriteRule ^ index.php [L]


Keep in mind that rewrites can be frustratingly hard to debug, but logging can help.  Also make sure you are using rewrites and not redirects.  Mixing mod_rewrite and mod_alias in same .htaccess will cause all sorts of grief because of process order.