Travelers looking to stay in the center of this beautiful city can't do better than booking through Brigolante Guest Apartments. Rebecca is a font of information about the area—customs, food, and what to see. She also manages several lovely properties in the countryside outside Assisi.
While you are in Assisi, I recommend taking a cooking class from Letizia Mattiacci at Madonna del Piatto. Letizia wrote the cookbook (literally) on Umbrian food, and travelers frequently report that cooking with her was a highlight of their trip to Umbria. She was also recently written up in the New York Times, bringing distinction to Umbrian cuisine. Those wanting more time amongst the olive groves may opt to stay at Letizia's B&B. Of special interest is her olive harvest vacation. More information on this, and a trip designed around Bevagna's medieval festival can be found at Smitten with Italy.
Where to go: For real St. Francis, head into the mountains to Eremo delle Carceri. Those interested in experiencing the Assisi of Roman days should read this article, by the incomporable Rebecca Winke, mentioned above.