Accomodation tips

if it were for myself, i would do:
stay in the restcamps in etosha np (okaukuejo, halali, fort namutoni) - there you can camp, or rent a room or a very nice chalet. and the camps are all INSIDE etosha and have a waterhole (especially great at okaukuejo) just infront of them.

in damarland, i would probably go for a nice lodge, like camp kipwe, or mowani moutain camp. not cheap, but not extremly expensive as well.

for sossusvlei, it depends how you are travelling around namibia. if you are self catering with a 4x4, i would stay at sesriem (early gate time) or sossus oasis (nice units). if you prefer a lodge, a great and "cheapish" place is sossusvlei lodge.

There's little point us recommending great places if they are full. Or if they are beyond your budget.

It would be more efficient to ask a local agent who knows the lodgings that are available.

Good and cheap places tend to go first in any market, so you will probably need good current knowledge to find places.

I agree about the Etosha rest camps. If you stay there, then Waterberg is probably superfluous.

I would use the night saved to stay in Swakopmund to break up the journey to Sossussvlie.

i would skip waterberg - that was probably the only place in namibia that did not impress us. in damaraland, aabadi mountain camp has a lovely location, although the dutch owners were not very friendly.

Hi Ilaria
We visited the Waterberg area a couple of years ago. We wanted to visit the Cheetah Conservation Fund which is on the D2440 off the road running north from Otjiwarongo, north of Windhoek and looked for a place which was close. We found Padberg Bed and Breakfast which is a farm run by Piet and his daughter (whose name I cannot remember). They provided a very clean, cool room in the courtyard and excellent breakfast and supper (and very kindly threw in lunch for us) plus a bottle of wine with supper all for very an extremely reasonable rate.
I think their website is not working at present (it's just possible they've gone out of business) but you might find more details on a search with Google. I think their telephone number is 00 264 67 306 238.
Hope that helps, and have a good trip.
Anna