If it can be installed using an override, you should do so.
To see if overrides are supported in a directory, look for the subdirectory "classic." As of 1.3.7/1.3.8, you'll see it in
./includes/languages/classic
./includes/languages/english/classic
./includes/languages/english/extra_definitions/classic
./includes/languages/english/html_includes/classic
./includes/languages/english/modules/order_total/classic
./includes/languages/english/modules/payment/classic
./includes/languages/english/modules/shipping/classic
./includes/modules/classic
./includes/modules/sideboxes/classic
./includes/templates/classic
this means the directory can be overridden. Where you see "classsic," create your own subdirectory with the name of your own template. For instance, in templates, if your template is named "custom," if you are overriding a file in includes/modules, you would create
./includes/modules/custom/
and create the file there. Keep with this strategy, and your upgrade will be less painful.
and put
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