The issue that you’re running into is that there is no such thing as a “standard J2EE project structure”, and there never has been. It’s simply not any any specification, anywhere.
As a result, there are many project styles in use in various areas. From a practicality standpoint, I simply use whatever structure is most expiedient with the tool / process I’m using at the moment as this allows me to focus on “development”, not on “set up”. Interestingly, this is why Ruby on Rails is so popular; it simply dictates how everything works and people just do it that way. Very efficient. In Java, people seem to like to worry about such minor issues and want things “just so” before they can get to work. Rather odd, really.
MyEclipse conforms to a “defacto standard” of simply setting up projects like their unarchived deployment targets (ie. WAR, EJB jar, EAR), which is common in many tools and deployers. For more information on how projects work in MyEclipse, please see the Documentation section. The Working with Web Projects quickstart is a good starting point.
Hope that helps.