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The progress is assigned to each issue manually in a custom field, and aggregated for parent issues.

You can use any numeric JIRA custom field to store the current progress % – a value from 0 to 100.

If the issue does not have sub-issues:

If the issue's Resolution field is not empty, and Apply Resolution is turned on, the progress is 100%.
If the issue's Custom Field value is not empty and is between 0 and 100, it's considered as the completion progress in percents.
If the issue's Custom Field value is less than 0, the progress is 0%, if greater than 100, the progress is 100%.
Otherwise, the progress is undefined, so such issue neither shows any progress, nor affects progress of its parent issue.

If the issue does have sub-issues:

If the issue's Resolution field is not empty, and Apply Resolution is turned on, the progress is 100% – regardless of the sub-issues progress.
If the issue's Custom Field value is not empty, it's considered as that issue's completion progress in percents (from 0 to 100) – regardless of the sub-issues progress.
Otherwise, sub-issues progress is aggregated sum of progress with chosen weights.

Custom field named Complete, total progress is based on All Sub-Issues Are Equal, and Apply Resolution is turned on.

Structure Plugin for JIRA - Version 3.1 > Progress Based on Percent Field > custom-or-resolution-settings.png

Column Configuration

Structure Plugin for JIRA - Version 3.1 > Progress Based on Percent Field > custom-or-resolution.png

Sample Structure

Issue	Explanation	Progress
Sub-sub-issue 1.1	This issue is 50% complete as specified by custom field	50%
Sub-sub-issue 1.2	This issue is resolved (indicated by the green mark) - so it is complete, even if "Complete" field is empty	100%
Sub-sub-issue 1.3	This issue has no progress information (neither "Resolution" nor "Complete" fields), so progress is undefined and not counted at all.	n/a
Sub-sub-issue 1.4	This issue has 0 "Complete" value, which means it's 0% complete	0%
Sub-issue 1	It has two four sub-issues, but 1.3 is ignored. So the total progress is average of the rest: (50 + 100 + 0) / 3	50%
Sub-issue 2	The issue is 25% complete as specified by custom field	25%
Top issue	It has two sub-issues: sub-issue 1 is 50% done and sub-issue 2 is 25% done. So the progress is average between two (25 + 50) / 2	38%

Custom field named Complete, total progress is based on the field Story Points, and Apply Resolution is turned on.

Structure Plugin for JIRA - Version 3.1 > Progress Based on Percent Field > custom-or-resolution-x-story-points-settings.png

Column Configuration

Structure Plugin for JIRA - Version 3.1 > Progress Based on Percent Field > custom-or-resolution-x-story-points.png

Sample Structure

Issue	Explanation	Progress
Sub-sub-issue 1.1	This issue is 50% complete as specified by custom field and has 2 story points	50%
Sub-sub-issue 1.2	This issue is resolved (indicated by the green mark) - so it is complete, even if "Complete" field is empty and has 3 stroy points	100%
Sub-sub-issue 1.3	This issue has no progress information (neither "Resolution" nor "Complete" fields), so progress is undefined and not counted at all.	n/a
Sub-sub-issue 1.4	This issue has 0 "Complete" value, which means it's 0% complete. It has no story points, so it's counted as mean of 2 and 3 = 2.5	0%
Sub-issue 1	It has two four sub-issues, but 1.3 is ignored. So the total progress is weighted average of the rest: (50 x 2 + 100 x 3 + 0 x 2.5) / (2 + 3 + 2.5)	53%
Sub-issue 2	The issue is 25% complete as specified by custom field and has 1 story point	25%
Top issue	It has two sub-issues: sub-issue 1 is 53% done and sub-issue 2 is 25% done. So the progress is calculated as (53 x 7.5 + 25 x 1) / (7.5 + 1)	50%