I'd make a copy of the alpha theme and rename it. Then I'd search for the term alpha within the scope of this new theme and alter it correspondingly.
Within the directory content you've already got some css files. I'd suggest to have a closer look at these to figure out how theme variables are used.
If you want to change the html structure of SmartStore.NET you need to take a closer look at the views (within the views directory). To overewrite them
on theme level just copy them into the views directory within your theme. Keep in mind the views in your theme have to be in the same subdirectory as the
views within the views directory.
So if you want to change the output of e.g. a blog post just create the directory blog within the views directory of your theme and copy the cshtml file that
renders the blog post there.
MyTheme/Views/Blog/PlogPost.cshtml
You probably have downloaded the web package. You need to download SmartStoreNET.Source.2.0.2.zip
Regards