We followed a mixed strategy. Define and manage backlogs using Greenhopper. Tests are defined as normal Jira items and linked to the backlog items (with link as 'is tested by') and closure of the linked testcases from the CI system automatically via SOAP interface.
If you are a fan of Executable Specification or FIT like test (http://fit.c2.com/) there are another interesting alternative. The product is called Greenpepper and those kind of test can be linked to your user story in Greenhopper. The product suite as been develop by Pyxis Technologies, the initial developer of Greenhopper and is there since many years now. You may have a look at it
I asked a similar question a couple of days ago: https://answers.atlassian.com/questions/60742/how-to-implement-qa-time-estimate-in-a-simple-manner. We ended up implementing QA/tests as a sub issue type that is added to the parent issues.
...PermissionsStartOnly=true User=www-data Group=www-data ExecStart=/opt/jira/bin/startup.sh ExecStop=/opt/jira/bin/shutdown.sh TimeoutStartSec=120 TimeoutStopSec=600 PrivateTmp=true [Install] WantedBy...
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