The BPS plugin should be installed on each/every site so that each site has all of the BPS plugin security features installed: Login Security, htaccess Firewalls, etc. See the forum topic link below for how to add htaccess code to the root site’s htaccess file so that it does not affect your other subdirectory sites htaccess files/code/rules: blog and kb.
http://forum.ait-pro.com/forums/topic/htaccess-files-for-multiple-website-domains/
Example:
# WP REWRITE LOOP START RewriteEngine On RewriteBase / RewriteRule ^index\.php$ - [L] # Do not apply rules to other child websites & # do not log errors for these child sites RewriteRule ^blog/ - [L] RewriteRule ^kb/ - [L]