Could you provide more details?
Here are some comments based on your note however:
1) AAT is not used to install an application. Installation is done either from the Admin Console (Web console for AEs, Application console for AE); or using SEAppInstall.bat for AEs (command line). This will be similar to what you do with JBoss.
2) AAT is needed if you need to modify the .ear file.
3) What did you use to build the .ear file in the first place? Is it fully compliant with the FCS of J2EE V1.2? You may want to use AAT to construct "new" WAR and EAR files.
Author of Enterprise Java (tm) Programming with IBM Websphere