To keep your issues ranked in the same order in JIRA Agile and Structure, you need to use a synchronizer.
If you don't already have a JIRA Agile synchronizer running on your structure, you'll need to set one up.
Here's a useful reference for the synchronizer - https://wiki.almworks.com/display/structure/JIRA+Agile+%28GreenHopper%29+Synchronizer
If you are already using a synchronizer and you are not seeing the desired results, please check that you have configured it to use the same rank field as your JIRA Agile project.
Hope that helps,
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