Copying a file into the server/xxx/deploy directory should deploy it after the server is running.
Do you want to change the configuration in the EAR file while the server is running and have it hot deploy? You should be able to do this with an exploded directory structure. Deploy the application as a directory structure with the top-level directory having the same name as what you would have if it were an archive (for example myarchive.ear). Then you can change your configuration and touch (or update) the META-INF/application.xml file to trigger a redeploy. If you have any WARs or JARs under the ear, you may want those to be exploded directory structures too.