This week's book giveaway is in the OCAJP 8 forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide and have Edward Finegan & Robert Liguori on-line! See this thread for details.
By "vaj", I assume that you mean VisualAge for Java... Firstly, no matter what IDE you use, you should probably never rely on the IDE to do your build. Use Ant or Maven to do your build, but don't use the IDE's build facility. (Of course, if your IDE supports Ant builds, then that's okay--but in this case, VAJ doesn't support Ant builds, so don't use VAJ to do your build.) The problem with VAJ is that it doesn't keep real file artifacts for the stuff it builds. To get real files (which you need for Ant) you have to export stuff, which introduces a manual step that I don't like dealing with. I recommend getting away from VAJ and to use an IDE that keeps real files. I recommend that you switch to Eclipse because it is very similar to VAJ. But if you insist on using VAJ, then you must export your files, then use Ant to do your builds. Once you've got Ant or Maven doing your builds, deploying to Tomcat (or any other server) is a snap. Just compile your code, WAR it up, then copy the WAR file to Tomcat's webapp directory.