It would be helpful to know the JDev version you're using here so we can help diagnose the issue.
It should be as simple as right clicking on the JAR and selecting "Add to project".
Sanity check: within the resource palette are you able to open the ADF Library JAR to see its contents? If yes this means it will be a valid ADF Library JAR, if not we need to look at your deployment process.
When you say you see the XML files for the EOs & VOs do you mean in the resource palette? Never mind, let's take a step back.
Via the following link this is what you should see for a Model project ADF Library JAR that contains EO/VOs etc:
If you were to right click on the JAR this is what options you should see:
I'd suggest you're still doing something wrong when you create the ADF Library JAR. To assist you via this link:
...you'll find a previous workspace/project I've setup. If you right click on the Model project look to the Deployment options you'll see an ADF Library deployment profile called "Model_Model_adflib". If you exit out of the preferences, right click Deploy -> select Model_Model_adflib, the appropriate ADF Lib JAR will be created under Model/Model/deploy. Returning to JDev and the Resource Palette, add a file system connection to this deploy directory, then you should see what I see above.
I guess you've deployed it to a "normal" jar file and not to an "ADF Library" jar file. Create a new deployment profile for the model project using ADF Library Jar file type (and not a plain Jar file type), deploy it, and then check out from the file system connection. You should be able to add then.