I'm using the development version (0.9.1.4b) of W3 Total Cache due to the nginx support. It seems to be working well despite some self-induced APC issues.
My main question is proper use of the nginx.conf file in my public root folder. I've set up my server as per the standard ubuntu nginx configuration of using a master nginx file in /usr/local/nginx/conf/nginx.conf and a domain specific configuration in /usr/local/nginx/sites-enabled/* (symlinked to sites-available). What I'm not sure about is how all of this interacts (or doesn't) with the nginx.conf that W3TC creates in my public folder.
Should I be manually adding the nginx rewrite rules to my domain specific config file? Or is there some better way to handle this? Thanks for the advice!