Issue links and sub-tasks are completely different from the "sub-issue" functionality of Structure. There are multiple syncs provided by Structure that can allow you to look for issues linked to those in a structure (whether by issue link or sub-task to parent relationship) and have them added to the structure, as well as have them added as sub-issues of those issues in the structure. You can also use syncs to link issues in the structure together, or even remove issue links between issues.
However, the functionality of Structure's hierarchy/indentation is completely read-only. You are not making any permanent changes to issues when you use Structure (unless you use the syncs I speak of above), and if you were to uninstall Structure your issues would be the same as they were before the install.
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