A few questions:
0) What version of MyEclipse, Eclipse, and OS are you using? What is the name of the tool that is marked invalid?
1) Are you using XDoclet for EJB code generation and deployment maintenance?
2) How do you know your having trouble with the META-INF contents not being deployed? If you used the MyEclipse EJB Project Wizard it should have created a META-INF directory. If you’re using XDoclet for you EJB creation then it will create and maintain your ejb-jar.xml file.
3) If you’re not using XDoclet then simply create a /META-INF folder under your EJB Project’s src folder. Then manually create and edit an ejb-jar.xml file. I’m a proponent of step #2, using XDoclet.
Michael
MyEclipse Support