Should I create user stories as super tasks and then create subtasks with the actual
 tasks/requirements?

Yes. It is very convenient because you can easily see why a certain task was performed. Besides, this approaches lets you to track the progress of every user story. 

 Should I estimate super tasks/user stories, or only the sub tasks?

From my experience, the smaller a task is the easier is to estimate it. Small estimations also tend to be more accurate. The estimation of a user story is the sum of its subtasks' estimations. Thus the story estimation is more fair, accurate and sensible. 

P.S. Here are some useful links on scrum and Jira:

- [With agile, what do when a user story doesn't get completed in an iteration?][1]
- [How do you keep track of a requirements document on an agile team?][2]


 [1]: http://programmers.stackexchange.com/questions/107774/with-agile-what-do-when-a-user-story-doesnt-get-completed-in-an-iteration/107776
 [2]: http://programmers.stackexchange.com/questions/177786/how-do-you-keep-track-of-a-requirements-document-on-an-agile-team/177911