Currently when we create a new subtask, it has its own effort estimate which is independent of the parent task estimate. Yet in most (not all) cases a subtask should be implemented within the overall effort estimate of the parent task.

This is leading to a fair number of issues in terms of being able to figure out the deviations from estimates. In the scenario we use Jira, subtasks are simply detailed tasks of the parent task. Thus the estimate for the parent task is supposed to be inclusive of the time taken for itself (and all the subtasks).

The following options are possible options :

a. Do not allow estimation for subtask. Add up the logged work for the parent task and all the subtasks to reflect the total time spent on the parent task.
b. Add a field to the parent task (e.g. total time spent) which would include time logged against subtasks as well. Use this field in the Time Tracking Report (where perhaps only parent tasks could be shown)
c. Similar to "Log Work" screen which automatically reduces the "Pending Time" based on the amount of work logged (but also allows the existing value to be retained using a radio button), the creation of a subtask should allow for a reduction of the "Estimated effort" for the parent task (by default) and yet allow the such a reduction to not be made (using say a radio button).