This week's book giveaway is in the OCPJP forum. We're giving away four copies of OCA/OCP Java SE 7 Programmer I & II Study Guide and have Kathy Sierra & Bert Bates on-line! See this thread for details.
The structure of a J2EE web application is the same regardless of which tool you're using to administer it. If your Internet Service Provider told you to create a WEB-INF directory in a particular place, I would tend to believe them and do as they tell you.