The best way to upgrade your template, would be to create a backup of it, and then copy the entire new template from the version you are upgrading to into your themes new folder. Once that is done, copy *only* the files you have customized back into the theme folder, allowing overwrite.

Once this is done, you can go through our change log and decide yourself which updates need to be applied (at your preference) to your customized files.

Template changes are listed here.