Which htaccess modify for SEO?

Hi, I have WP installed in a root’s subdirectory, like this /wp.
There is one /.htaccess in the root and another one in the subdirectory /wp/.htaccess
My doubt is which of these must I modify for SEO purposes? (enable caching, enabling Gzip, enabling keep-alive and so on)

The root’s one is valid for the whole site?

Thanks in advance!