Having just crossed from Namibia to Botswana by car, I thought I would describe the experience.

First, you should have a letter from your car rental agency with full details regard you car, and authorization to leave Namibia with the car,
you will cross at Ngoma Bridge, a very small crossing

as you arrive, there is a low building on your right. No indication that this is Immigration stop, but it is. You should go in and have your passport stamped indicating that you are leaving the country.

futher on there is a very small, unstaffed, hut. Here you must sign a book (left on a small table and leave info from the car rental agency (engine number, etc.)

on leaving this behind, you drive across to Botswana, a medium size hut, again with no signs indicating that it is Immigration - customs
here they will check your passport, and charge you tax - ours was 102 pula. Payable by credit card, so no need to worry about exchange

leavin, we were asked to wash the soles of our shoes
then on to Chobe Park, where they will once again ask for various papers
Finally you leave

as someone who has travelled to many places, we still found this all confusing, since nothing is marked anywhere. So we ended up driving back and forth, feeling stupid. Bonne chance et bon courage to the rest of you.