It breaks my entire site! CSS and JS file can't...

First of all, WP permalinks (Settings > Permalink) should be enabled and “work” on your site. Following this, make sure you use Apache webserver and not Nginx, Windows (IIS) or Multi-site as they need manual configuration. If they are OK it means you have a customized htaccess. Open your htaccess via a FTP program and follow below check list:

RewriteEngine On
RewriteBase / #OR YOUR DIRECTORY NAME
RewriteRule ^index\.php$ - [L]
#[Probably HMWP LINES]
RewriteCond %{REQUEST_FILENAME} !-f
RewriteCond %{REQUEST_FILENAME} !-d
RewriteRule . /index.php [L]

RewriteCond %{REQUEST_FILENAME} !-f

RewriteCond [Something] 
[One or more RewriteCond [Something]]
RewriteRule .* index.php [L]

You may need to enable customized htaccess (in HMWP settings page) or change its permission to read-only to avoid WP updating htaccess frequently.