'Unzipping the application' - Are you referring to unzipping WAR/EAR file. In that case, yes the jars will be placed inside the /WEB-INF directory of the extracted one.
The
J2EE IDEs(eclipse, netbeans etc) however support, to have
java libraries (.jars) to be linked with the code base by adding the .jar to the build path. But it is advisable to have it in WEB-INF if the jar is specific for your application, the reason being when you export the Source code to WAR, it will include only the jars inside your WEB-INF directory.