You’re not supposed to modify the Dashboard.
It’s recommended to create custom post types for content organisation and a top-level feature plugin for more complex options and settings. You can also use the Customizer to allow theme changes. A theme might already have these settings, so you could add some meta boxes with general help and how-to tutorials. You can also change the admin theme.
Note that a major WordPress version is coming really soon – 5.0 – and a feature plugin to make the admin theme dark is already submitted for consideration in core. Any Dashboard-changing plugin you might find, could be invalidated by this major version.
Also note that any Dashboard-changing plugin you might find is usually based on hacks and styling overrides.