Well, with any command, you have a basic reference right in the terminal: you just say "man <whatever>" e.g. "man apt-get". You pick up various things over time, and the Internet is a great help here. Otherwise, just get your hands dirty - but make backups before changing files.
It might help to remember that "Linux" really only refers to the kernel, the "engine" under the hood. Applications like apt-get, or X-Windows and anything running under are not core and can be changed. Even the shell where you enter commands (usually "bash") is optional, though Ubuntu installs a lot of these applications to make the system usable by mere mortals.
The various "package managers" - systems for installing and deleting applications - are among the major differences between competing Linux systems. Red Hat, Mandriva & some others use the Red Hat system (RPM), SuSE has its own system, while Debian-based systems such as Ubuntu use the DPKG system. The "apt" commands are a friendlier layer on top of the "dpkg" commands", and there are also X-Windows applications that make it even easier, such as Synaptic or the new Ubuntu Software Centre.
I admit to having been a little confused by "sudo" at first: put it in front of any command, and that command runs with root privileges, just by entering your own password. Isn't that a security risk? Yes, it is, but it's not automatically enabled for all users, just the first user you create during installation. The alternative to that is logging in as root, which could be seen as an even greater risk, since the root user really can do anything, including things that can kill the installation stone dead - and you can get blasé and careless about it. You can use "sudo" to enable the root account if you want, but I wouldn't, since "sudo" does the same job, one command at a time.
edit: I should add that the location of those files is not the kind of thing you'd figure out by yourself - except for the general idea that they'd be in the place generally recommended for an application's working files i.e. under /var. I don't think /var/lib/apt is ideal, though - I'd say /var/cache/apt would be better, alongside the downloaded packages. In other words, while there are guidelines, the exact location is set by the developer, not dictated by Linux itself.
Last edited by bnt; 18th Nov 2009 at 19:49.