0. What do you mean by “J2EE Project”, there are 3 project types listed under “J2EE”. Are you talking about a Web, EJB or Enterprise Project? Also I need more detail about your project setup and you haven’t answered the questions asked in the Posting Guidelines at the top of this forum, those can sometimes give us key info that helps but in this case it sounds more like a slight misconfiguration than a major install problem.
1. I think you are talking about an Enterprise Project right? In that case it’s called “Generate Module Manifests”. See section 9.1 of the Enterprise Project Quickstart, see Figure 31: http://myeclipseide.com/enterpriseworkbench/help/index.jsp?topic=/com.genuitec.myeclipse.doc/html/quickstarts/earprojects/index.html
2. This depends entirely on the type of libraries and how they are added to your build path or placed in your project OR dependent projects. I will need you to explain in detail what your project setup is like, where your libs live, how you have added them to your build path and the behavior your expect, that is not happening. Also note that if you are trying to deploy libs from dependent projects you must export those JARs from those projects to get them picked up, this allows you to select which ones get deployed (Gives more control to user).