I'm not sure what those nginx rules do, but here's my guess:
Match ^/files/$ Rewrite /index.php
RequestURI exists Return
Match ^/[_0-9a-zA-Z-]+(/wp-.*) Rewrite /$1
Match ^/[_0-9a-zA-Z-]+(/.*\.php)$ Rewrite /$1
The first wp-admin line can be ignored.
You can learn to write these rules by learning 'regular expressions'. Google for them to see what they are and can do. Also take a look at file config/toolkit.conf inside the Hiawatha source package. This gives you an overview of what the UrlToolkit can do. For the rest, see the manual page.