I have created a template in /includes/templates directory called MYCUSTOM. So the directory path is /includes/templates/MYCUSTOM

In the Admin area, I clicked Tools>Layout Boxes Controller. The screen shows the Boxes Path as /includes/modules/ …
I am not going to reset it to default.

Let’s say, after making changes to the LEFT/RIGHT COLUMN Status, LEFT/RIGHT Column, LEFT/RIGHT COLUMN Sort Order, SINGLE COLUMN Sort Order and SINGLE COLUMN Status for all the box file names, what steps should I take next in order to retain the settings when there is an upgrading of the software.
Currently I am using v1.3.9h.

I appreciate the response. Thanks.

NOTE: This was wrongly posted to Post relating to Minisite.