From Hosting Knowledgebase: "In order to also set up your main domain to use a subdirectory on your hosting account you will need to set up a redirect in the .htaccess file in the public_html folder so that the server knows that any request for your main domain will be redirected to a subdirectory on public_html. " Will the above action have any adverse effect on SEO for the primary domain site? Thanks.
Should not be any problem, you hosting account is already a subfolder below the web server. The DNS channels your site to the correct place. It will not affect your ranking, Google will never find out you're in a subfolder (and doesn't care anyway).