Unlike Mac OS 9, which pretty much let you put your files and programs wherever you wanted as long as you left System and Finder inside the System Folder, Mac OS X has certain expectations regarding paths, the hierarchy of folders leading to a particular spot on your startup disk. The distinction between your personal files -- your documents, music, email, bookmarks, preferences & settings -- and everything else that helps your computer run can be stated simply: if it's in your Home folder, it's "your stuff," and if it's outside your Home folder, it's universal to the computer (or it belongs to your spouse/kids/etc.).
To get to your Home folder quickly, you can click the house icon in the sidebar of any Finder window; choose "Home" from the Go menu in the Finder, or hit Cmd-Shift-H. Once there you'll notice a few folders, including Documents, Desktop and Library. You may think "I don't like books. Why do I need a whole folder for a Library?" and be tempted to tuck it away in a "Misc" or "Stuff To Throw Out" folder. Don't be surprised, if you do, that you can no longer log into your computer -- Library has to stay exactly where it is, since it contains all your preferences and application settings. Likewise, there are some folders in Documents that have to stay put, particularly (if you use Microsoft Office) the Microsoft User Data folder.
Other than the preconfigured folders, your Home folder is pretty much yours to manage as you choose; you aren't limited to storing documents in Documents. Need a folder for Projects? Go ahead and make one (Cmd-Shift-N for a new folder), just don't get funky with the original items unless you know what you're doing.
One more tip on home folders: sometimes you'll see the notation "~/Desktop" or something similar in documentation for software, telling you where files will be installed. That "~" (it's called a tilde) is UNIX shorthand for the active user's home folder -- it expands to "/Users/myname/" when used in the Terminal, and whenever you see it you should assume it's talking about the place for your stuff.