w3cache plugin with cloudflare

I have installed W3 cache plugin and using cloudflare.
Cloudflare works perfectly on main domain.
But I want to use it for all subdomains in my multisite.
I tried using it for http://mr.jasonalexis.com
Under general settings it shows "Disk enhanced page caching is not active. To enable it, add the following rules into the server configuration file (/home/jasonale/public_html/.htaccess) of the site above the WordPress directives"

When i click auto install it installs on subdomain but it changes setting on main domain and show this message on main domain.I think Its because the same htaccess file is used. and it overwrites the same file again adna again.
How to use cloudflare with w3cache plugin on multisite?