Are you speaking about a visa issued by the Government of Sudan (GOS), or a travel permit issued by the Government of South Sudan (GOSS)?
If you are entering South Sudan from Kenya, I believe that the document you need to have is a GOSS travel permit, not a GOS visa (although the GOS visa may also be necessary if you plan to continue your travel up to the Northern part of Sudan). The GOSS travel permit is a stand-alone document (not a stamp in your passport) that is issued by the GOSS office in Nairobi. When you present the GOSS travel permit upon entry to the south, you then receive a GOS stamp in your passport - plus, of course, the GOSS permit is also stamped.
I flew into Juba two weeks ago from Nairobi, and this was the procedure that I followed. As far as I know, this procedure has been in place for several years now. I am not sure what kind of reception you would get upon entering the south if you only presented a GOS visa.
Of course, if you plan to enter the North (e.g. fly to Khartoum), then a GOSS document is not needed.
You might also want to have a look at this discussion about travel in South Sudan: Sudan to Kenya
. I don't think now is a good time to visit South Sudan, unless you plan to be out of the South no later than December 1.