Hi,
First, if you've done your modifications via the interfaces in Display->Views and in the config for the CSS, you won't loose anything when updating/upgrading. However, if you did your modifications directly in the files you would indeed loose then when updating/upgrading.
If you have the same version 1.5.3 than the one you downloaded, you can indeed just copy the files. You will also missing the plugins included in the business edition but you can zip the files of the plugins in back/extensions and install them via joomla separately.
If you have another version installed, then it will require database modifications which are done during the install process so just copying the files won't be possible.