While I’m not a frequent Dreamweaver user, lots of people have a great deal of success with it. I think you probably have the right idea, but what you might need to do is restrict your editing to just what is inside a specific theme directory. The only files you will need to edit for your site would be files in whatever theme you chose to use. For example, if you installed and activated the Graphene theme, and decided that you want to modify it to better suit your needs, you would only want to edit files located in /wp-content/themes/graphene. If you are creating your own theme, your working directory would be /wp-content/themes/your_theme.
So in short, customizing your sites theme using Dreamweaver, would probably mean editing only files found inside of your actual (active) theme directory. Not /wp-content/themes, but /wp-content/themes/your_theme_name. Editing anything else will in most cases, cause issues and errors with WordPress.