[cherie]

Most of your changes will be how the store looks so create a separate skin directory with nothing in it except the files you customize plus your own css/altskin.css. If you want to change a tpl, copy it from common_files into the same place in your new skin directory. Your upgrade should go smoothly but you will have to manually patch any tpl files in your custom skin directory that you copied from common_files.

Or if you want to start with a built-in skin as your starting point, such as Ideal Responsive, copy ideal_responsive to a new skin directory with your new name, adjust altskin.ini, and adjust the files as needed. When you upgrade you'll have to manually patch your skin files using the diff files from the upgrade for ideal_responsive.

If you must make a change to a php file, back it up and comment your changes so you can easily compare (diff) the files if you need to manually patch them during an upgrade.