You might want to go through this introductory exercise in maven : http://maven.apache.org/guides/getting-started/maven-in-five-minutes.html
What you are describing is possible, but takes some work and understanding of maven to accomplish. If you would like to convert your project to maven, it might take a bit more work than just changing the project to the maven structure in eclipse. An example maven project for App Engine is here : https://github.com/GoogleCloudPlatform/appengine-guestbook-java . Some App Engine specific docs on maven are here : https://developers.google.com/appengine/docs/java/tools/maven