One of the things that is always challenging with online sites using a 3rd party software like CFWebstore is updating to new versions. Since the application is basically nothing more than a huge collection of text files, there's no real way to provide some kind of executable updater program. So performing an upgrade usually involves copying over all the changed text files, while attempting to preserve any changes you may have made to the code. Typically this involves at a minimum your layout files, but a large percentage of stores have changes in other pages as well that you want to be sure that you don't overwrite. By far the best way to do upgrades that keep all your changes is to use a file comparison tool. There are a number of good products out there, but one of the most popular ones is
ExamDiff Pro. ExamDiff does come in a free version as well, but you'll want the Pro version for the full directory comparison and powerful customization options that it has. For the low registration price of $35, you'll find it well worth the time savings you will get when doing upgrades. This tutorial will help to show you how I do upgrades, you can certainly use a different process that best suits your own work flow, but this should at least get you started.