the xml files are used to create the tables when a plugin is first installed. If you need to modify tables once a plugin is installed (i.e. as part of an upgrade), then you need to create/update the update.php file with php that triggers the changes. Those changes can be generated from within the xmldb editor. See any plugin with an upgrade.php for what this code looks lile.
General developer forum
I need help understanding how/where Moodle keeps its database
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