I am planning 4 weeks in Sicily in October and we will do all our travel by bus.
We will stay in Erice, Trapani, Palermo,Modica,Syracusa, Taormina, Catania.
I have heard that Syracusa in the old city is a great place to base yourself and see southern Sicily
some great b & b's we found. Palazzo del Sale in Syracusa
B & B Palazzo Cavaliera, Modica
B & B Mamma Maria, Taormina
Butera 28 apartments in Palermo
www.icoloridalvento.it A hotel on the seafront in Trapani at 75 euro a night.
I am not sure what your budget is but these were some of the best rates in the best areas we could find.
They all have a minibar/fridge and are very central to the bus station and all in the historical area of the City.
Hope this helps