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In any case, you'll need to synchronize your .feature files to Jira so that you can have visibility of them and report results against them.

The overall flow would be something like this:

1. look at the existing "requirement"/Story issue keys to guide your testing; keep their issue keys
2. specify Cucumber/Gherkin .feature files in your IDE supporting Cypress and store it in Git, for example
3. implement the code related to Gherkin statements/steps and store it in Git, for example
4. import/synchronize the .feature files to Xray to provision or update corresponding Test entities
5. export/generate .feature files from Jira, so that they contain references to Tests and requirements in Jira
6. checkout the Cypress related code from Git
7. run the tests in the CI
8. import the results back to Jira

Usually, you would start by having a Story, or similar (e.g. "requirement"), to describe the behavior of a certain feature and use that to drive your testing. 

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