Managing java files and packages

Hi,
I am just starting out with java and have reached the stage where I want to store my files in packages and the correct directory structure. I have read through the sun link below and have a question they seam to miss. They say that .java and .class files should be kept in separate places. ie sources and classes directories with the package directory names below. But I have found that unless you have the .class files you are referencing in the same directory as the .java files when you come to compile you will get an error so they have to be stored in the same directory???.. Does this make sence or have I gotten it all wrong.
Thanks
Joolz
http://java.sun.com/docs/books/tutorial/java/interpack/managingfiles.html

You should put path containing your classes in your classpath. There is a -classpath option in javac.

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