You can configure rules to trigger a fee addition to a given order, examples of this are adding a shipping fee if the delivery is overseas or charge extra for cash on delivery payment method.
Commerce fees will add a new line item to the order with the arbitrary amount configured.
INSTALLATION
Place this module directory in your "modules" folder (this will usually be "sites/all/modules/").
Don't install your module in Drupal core's "modules" folder, since that will cause problems and is bad practice in general.
If "sites/all/modules" doesn't exist yet, just create it.
Enable the module.
Visit "admin/commerce/config/fees" to learn about the various settings.
DOCUMENTATION
Go to admin/commerce/config/fees and add a new fee type