I don't know where your code is but this:
mysite.com/mytemplate/includes/modules/sideboxes/mytemplate/

is not a valid path ...

you see the:
/your_secret_admin
/download
/images
/includes

Now go to:
/includes/modules/sideboxes

copy the file:
/includes/modules/sideboxes/whats_new.php

to your templates and overrides directory for modules in:
/includes/modules/sideboxes/your_template_dir/whats_new.php

and then add the customizations ...

follow the same method for the best_sellers.php ...