If you are using Eclipose, I recommend that you install the JBoss Tools plugin and read through the JBoss Tools documentation - they contain many tutorials on using Toolks to develop and deploy applications.
Personally, I recommend that you do not use any IDEs, tools or wizards and instead use only a text editor (using Eclipse as a text editor is fine) to edit all files, inlcuding source files and configuration files. Then use command line tools (javac, jar, etc.) to build, package and deploy your apps. I guess that it would be alright to use Ant or Maven to do some of that for you, provided you understand exactly what they are doing. Only after that would I say that you are ready to do Java EE development with Eclipse. I say this because at this point is appears that you are fighting with Eclipse rather than accomplishing your goal of developing Java EE apps.