Copy the 'Standard' theme into another folder. Make your changes to the CustomerHeader.dtl, CustomerSmallHeader.dtl, and so on ... and create a new theme in your mysql database.
Then you can choose the theme as 'Standard' in your OTRS configuration.

To paste it into your database just login in to your mysql server and then do the following.

use otrs;
INSERT INTO theme;
(id, theme, valid_id, create_time, create_by, change_time, change_by)
VALUES
(3, 'Theme Name', 1, current_timestamp, 1, current_timestamp, 1);