Cs-Cart File To Sub-Folder In Host

now I moved my cs-cart file from root to sub-folder and I edit the htaccess file . and everything is ok and website works well.

now I have htaccess in subfolder and htaccess in root contan [code to make primary domain read from subfloder

RewriteEngine on
RewriteCond %{HTTP_HOST} ^alphastore-kw.com$ [NC,OR]
RewriteCond %{HTTP_HOST} ^www.alphastore-kw.com$
RewriteCond %{REQUEST_URI} !alphastore-kw.com/
RewriteRule (.*) /alphastore-kw.com/$1 [L]

]. but I read cs-cart guidelines to make this {

  1. If the SEO add-on is enabled, open the .htaccess file located in the root directory of your store.

  2. Find the following line of code there:

    # RewriteBase /subdirectory
    can anyone please guide me how I can do that. because i tried to change htaccess subfolder to this
    # RewriteBase /subfoldername

does it will affect in our SEO and google indexing