Thaeris I have no idea how the GUI translates commands to the OS
It doesn't. It transmits commands to eopkg at the command line. Updating from eopkg just eliminates the middleman, and makes it easier to see what's going on and if necessary, to recover from a download time-out.
When you've tried it once, you'll see how easy it is. It doesn't take a software engineer to use the command line.
EDIT: A little more on this. The mirror is a remote server that exists to provide local downloads. They exist in various parts of the world. Someone in Australia, for example, doesn't need to download updates from France. (Just an example to make the point. I don't know where all the mirrors are.)
When the mirror server times out because of a huge download and maybe because it's overloaded, the Software Center doesn't handle the rejection very well. From the command-line, though, it's easy to see when the download progress stops.
When you see that happen, just press <Ctrl-C> to break out of the traffic jam, and press the up-arrow key to repeat the command you just entered, and press <Enter> to execute it again. It seldom takes more than one such restart to finish the downloads.
The command to upgrade from the command-line is
sudo eopkg up. As simple as that.