Imagine I was a search engine robot. I find your domain and begin indexing and come across a link to your subdomain. I go there and find an empty site. Your re-direct is hidden in your server settings so as far as I am concerned the sub-domain has no idexable material.
You could have a direct link to the sub-directory from your homepage but this will count as an internal link and not help your ranking.
If you want you sub-domains to rank well you need to buy some webspace and move the content overthere.
As to the redirect, what is it that isn't working? If I search for domain.com,
www.domain.com or
www.domain.com/index.html will I end up in the same place?
And the file is called .htaccess not .htaccess.txt - remove the extension and try again.