Staying in Hotel Latran will be your excellent choice if you want to spend a night in Cesky Krumlov. You can start your tour from this hotel and it will even be very close to one of the bus stops. Single room might be bit small, but it has everything you need and also it will be very cozy. One thing that bothered me little, was very thin walls - you might be hearing footsteps from hallways and people talking outside. But, other than that, it was so great here.