How do I plan my trip to Juba in Southern Sudan

I don't know what you are asking. Hotels, airlines, visas, something else?

Trip? From where? When will you go and how long will you be there?
Aside from civil war tearing up all the roads in and out, flooding from March to October, and a very high cost of living due to rapid growth of the city itself, if you still want to go there, you would generally fly from Nairobi.