Question

Should I disable sub-tasks to use Structure?

Answer

Not necessarily. While Structure plugin can be a good replacement for sub-tasks, they can be used in parallel — for example, if you want to try Structure on a single project without affecting other JIRA users.

Structure treats sub-tasks as any other issues. You can also install a Sub-Tasks Synchronizer, which makes sure that JIRA sub-tasks are positioned under their JIRA parent issues.