htaccess duplicate

Hi everyone,
It seems that I have 2 htacess file, one at the root and the other at “/www”. Both have different content as one was modified by W3TC and the other was created by me.
It seems that till now there is no conflict, but I was wondering what is the impact of having these 2 files.
Thanks,

http://wordpress.org/extend/plugins/w3-total-cache/