This week's book giveaway is in the OCAJP forum. We're giving away four copies of OCA Java SE 8 Programmer I Study Guide 1Z0-808 and have Jeanne Boyarsky & Scott Selikoff on-line! See this thread for details.
Having two different classes with the exact same fully qualified name in two different JARs is not a good idea, there is really no way to handle such a think easily. If you were dealing with javac or the java runtime directly, you could order the JARs in the classpath in such a way as to get the JAR (or directory) with the desired class to be earlier in the classpath. But with Eclipse and Maven you don't have that low level control over the classpath.
Why do you have two classes with the same fully qualified name? Perhaps if we knew that we could come up with a better scheme to accomplish the same goal (off hand I would say you probably want to use a factory pattern but it is hard to say without knowing your requirements.)