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:
