If you are using 1.3 and want to automatically document the top level package and all its subpackages, a good way is to copy, compile, and run the program JavadocRecurse.java
from the Javadoc FAQ page at:
http://java.sun.com/j2se/javadoc/faq.html#recursesource
1.3 does not have this feature built-in, though 1.4 does with the -subpackages option.
-Doug