You'll get better basic Java support in one of the Java-specific forums; they can talk you through compiling projects with external dependencies.
Maven certainly works, and it's how we build Struts itself, but w/o a decent grip on how Java works in the first place if anything goes wrong you'll be high and dry--it's good to understand the basics of how and why it works, which compiling "by hand" will give you.
When compiling it doesn't matter so much *where* the libraries are located, as long as they're available somehow, either by being on the classpath or via some other mechanism.
When running the webapp they have to be available to the application; in general you won't want them in the JRE/JDK lib dir *or* the app server's lib dir, but in the web-app-specific dir. More information about web app stuff is better asked about in the
servlet forum.