Most high-standard hotels are in Khartoum and Port Sudan, with limited options outside. Many upmarket hotels quote rates in US dollars and won't accept payment in Sudanese pounds; all other hotels quote in Sudanese pounds.
Cheaper options include lokandas (basic hotels) and family-run guesthouses.
All hotels will request a copy of each of your travel permit, passport and visa. Bring plenty of copies as hotels will keep them.