I don't have any experience with BPEL on Oracle WebLogic but according to this documentation a BPEL application is packaged as a standard EAR. I don't know exactly how your sources are structured under JDeveloper but you best option here to automate the packaging and the deployment of this EAR is IMO to use Ant (or Maven but if all this is totally new for you I would recommend using Ant).
Maybe this tutorial can help you to get started for the packaging part (basically, how to use the ear task). And for the deployment, I suggest to use the wldeploy Ant task (which wraps the weblogic.Deployer
utility). I've mentioned them in this recent answer.
Also have a look at this question, it seems that JDeveloper might have some support to achieve this task (but I have zero knowledge of it so I can't provide any guidance, JDeveloper is not really widely used).