System-wide proxies in CLI Ubuntu/Server must be set as environment variables.
Open the /etc/environment file with vi (or your favorite editor). This file stores the system-wide variables initialized upon boot.
Add the following lines, modifying appropriately. You must duplicate in both upper-case and lower-case because (unfortunately) some programs only look for one or the other:
apt-get, aptitude, etc. will not obey the environment variables when used normally with sudo. So separately configure them; create a file called 95proxies in /etc/apt/apt.conf.d/, and include the following: