Planning a route through the desert takes some coordination to make sure everything goes smoothly. Having a vehicle that can handle the terrain is the best way to get around the coastal areas and the canyons on your own. You can rent a car in Namibia here:
https://getrentacar.com/en-US/namibia . The site displays different models that are built for the long gravel stretches between the parks. You can find a 4x4 to handle the sections where the sand gets a bit thicker. This helps when you are carrying all your extra supplies across the remote regions.