Hi Inseok,
If I understand your question, the best way to run an EAP instance of JIRA is to use the Atlassian SDK as well.
So for example, the latest EAP version of JIRA is now 6.1-m02. You can get and start that version with:
atlas-run-standalone --product jira --version 6.1-m02 --jvmargs '-Datlassian.upm.on.demand=true'
(Previously, you would've had to install UPM 2.11 to be able to put UPM in OnDemand mode like this, but 6.1-m02 comes with 2.11, so no need for a separate UPM update step.)
Once it's running, you still need to add the query param in UPM to see the Atlassian Connect links in the UPM, such as the license token management link: ?upmDeveloper=true