Depends on your budget. If you can afford to the best way is to hire a vehicle and do it yourself. Make sure you use a reputable car-hire firm. Otherwise you can come back to me - I am an independent travel consultant based in the UK and specialise in Namibia and Uganda. I would require details of your budget and exactly what you want to do (i.e. wildlife, dunes, culture etc). I charge just US$25 per person and organise everything with the exception of flights.
If you are interested please send me an email using the SEND ME AN EMAIL link.