First off, welcome to the world of UNIX. You’ll probably be getting more help from command-line freaks like me than you ever got when you were still banging around with MacOS Classic.
The concept of different users exists to keep you from shooting yourself in the foot. There are different users with different levels of permissions, with root (is it called root in Mac, or is it Administrator?) having all power and the rest of them having enough power to manipulate the files and directories they own, or have been explicitly been given permission to modify.
Permission? Ownership? Yep, those concepts are straight from the UNIX that serves as a server OS, allowing whole corporations of people to use the same backroom mainframe without anyone stepping on anyone else’s toes.
But you don’t care about that. You care about using your machine without hassle. The concept of users can help you with that, too. Simply create a user distinct from root (or Administrator) and do most of your work as that, instead of signing in as root all the time.
What does that buy you? You no longer have to worry about formatting your hard drive by mistake, or nuking an important system file. You can no longer screw yourself out of a usable OS through your own fumblings, because the OS can protect itself from a non-root user. You can just use your machine as you always have, with the added bonus of security not being root buys you.
Security? Yep. As a non-root user, any programs you install are also non-root. That means they can’t damage your OS any more than you can. To speak techie, programs inherit the permissions of whoever installed them.
So, what if you want to fix an important file, but OS X bitches that you can’t 'cause you aren’t root? Simple: Log in as root (which in the command line involves running su, and I have no idea what the Apple folks gave you for the GUI equivalent), alter the file, and log out of root to return to your normal status. It’s like being Superman. He doesn’t wander around in blue spandex all the time because he doesn’t want to be constantly hassled, but when duty calls he drops the Clark Kent persona in the nearest phone booth and Does His Thing as the ultimate superuser. (Superuser, in fact, being the other name for root. ;))
So how do directories tie into this concept? Well, whole directories can be protected from tampering. You can set up a directory that’s between you and root: Nobody else can even see what’s inside it, let alone enter it. This means that no programs can futz with it, either (remember the inheritance principle). Directories also help you (and the programs you use) find things more easily, because everything `stays where it’s put’. That was once a GUI theme in the Mac world, but it’s always been a file theme in the UNIX world. Two great tastes that taste great together, as it were.
(Disclaimer: I’m a Linux fan, and MacOS X runs a BSD variant as its kernel. But the things I’ve talked about apply to all UNIX versions, right back to the 1970s.)