We are not trying to change our project methodology, even with X-Ray we follow the way how we are using Jira on projects. There are just small changes added by using X-Ray on the project:
Test cases - with X-Ray test cases are reported as Test issue types, test cases are linked to correct user stories so it is clear why they were created and what they should test. More test cases can be created for one user story.
Test Plan - issue type for administration added to Jira by X-Ray. There should be one Test Plan for each project and all test cases on the project should be linked to that Test Plan. Test Plan allows to PM to see general overview of all test cases created for the project and also overview of testing results.
Test Execution - issue type for administration added to Jira by X-Ray. There should be one Test Execution for each Feature Sprint and all test cases on the project should be linked to the correct Test Execution. It allows to PM to see general overview of all test cases created for the Feature Sprint and also overview of testing results.
Reporting bugs - as we are in development phase during Feature Sprints, we usually describe founded issue to Comments section and we move the user story to Rejected state and assign it to CE for fix. Bugs are reported by our QA Analysts when it is not clear what was the root cause for the bug and from UAT phase to Go-Live. It is possible to use another way for reporting bugs, but it must be always approved by PM.