1. If your sources.list are http then you use the http proxy in Acquire section, if sources.list are ftp, then you need to modify the http to ftp.
2. It is strange to me that you have a /etc/apt/apt.conf, as it is not present in the apt folder due to a more modular structure in BTr3 and kernel >= 3.x.x.
What you need to do is go to /etc/apt/apt.conf.d and create a file named, let's say 99my_proxy:
and save it, then reboot...
You could also use the 70debconf file and add the Acquire::http:roxy "http://usernameassword@<proxy_ip>:<proxy_port>/";
But try the first option first..It is more recommended., since if you alter any of the lines by accident within it, it will cause apt to be unstable and behave in an unwanted manner.