Store Commander includes an option so that when creating or modifying products in Store Commander, their link_rewrite is automatically created and updated.
If however the link_rewrite is not created or modified automatically, please check that the option in Store Commander > Tools > Settings > Catalog > SEO > Always use product name as link rewrite = 1
For PrestaShop version 1.6.x, this option has been removed from Store Commander because it now exists in PrestaShop backoffice > Preferences > Products > Force update of friendly URL.
Please note that the option is disabled by default.