If you want to your SQL as a source for your Jasper reports you can install Smart QL addon alongside Smart Reports. Since version 0.11.0 Smart Reports app contains built-in integration with Smart QL. It comes in form of Jira plugin which installs automatically with Smart Reports - it is called Smart-Reports Smart-QL integration. To enable it - simple ensure that Smart-Reports Smart-QL integration addon is enabled in your JIRA. You can do it in Addons managements.
If you want to disable the integration - disable the Smart Reports Smart QL integration addon.