Multiple nginx.conf files - how do choose?

I compiled nginx from source on Ubuntu 13.* as this is my first foray into NGINX. Once i got the server successfully up and running, I had troubles getting it to obey server contexts for a site I already had setup on the server (which was previously running under apache).

I originally modified a file cat /etc/nginx/nginx.conf which DID NOT affect server behavior. AFter reading some additional forums I located an additional nginx.conf file at:
/usr/local/nginx/conf/nginx.conf. Adding the server contexts to this helped. However, I'm wondering what the one under etc/nginx is, and noticed that there are also standalone serve context type files located in /etc/nginx/sites-available and sites-default (much like apache), but i edited these before the one at /usr/local and they didn't work either.

Can someone tell me what the best practice is for defining configuration, specifially server contexts, and why there are multiple locations/config files where this seems to be applicable? Again, the only one that affected server behavior seems to be the default one at /usr/local/nginx/conf/

Any insight from those more experienced would be very appreciated...