Just in case our friend is not doing a default installation...I suggest the following:
1. Read man hier -- if you're running Linux, open a terminal and type
and read the page that pops up. That will explain in excruciating detail all the typical directories -- most of the ones that will be installed when you install any major Linux distribution. If you're not running Linux, put that into google and see what comes up. You should get the same document.
2. The literature that best prepared me for setting up my own system was Running Linux by Welsh, Dalheimer et al. After reading that I felt like I totally knew what I was doing. It's also a great primer on the general "UNIX way".
Here's my basic explanation
/ -- the whole damn show. If you dont' tell your installer what partition to mount on / or /home, you should get an error and it should give you a chance to go back. If it doesn't, start over because it's probably incapable of doing anything unless you give it these mountpoints.
/home -- holds directories for each user to store data. Can include programs installed just for a particular user. Under this directory on my computer, you'll find /joel (me) and /megan (my wife).
/usr -- programs available to the whole system. /usr mainly holds data (e.g., libraries), source code and other good stuff; the binaries may be in /usr/bin or /usr/local/bin or they may be somewhere like /bin or /sbin.
Although some people recommend mount /usr on its own partition, its usually just fine to put in on the / partition with everything; /home should have its own partition.
The previous posts might not fit your situation if you have already chosen a distro. However, you control the level of customization you want mainly by choosing a distro. As the previous posters said, "your distro will do it for you." As I favor distros like Slackware that require customization for every install, I disagree that you should let the computer take care of it for you without you knowing what it's doing. A good middle ground is a distro that gives you options and is set up for either a custom install or a generic install. I recommend PCLinuxOS.
As an example, I did not like how Ubuntu just "took care of it for me." It seems that I was expected to have that attitude about everything else going on with the computer, too. I think you'll learn more if you have to take care of these details and the installer tells you what it's doing.