I would appreciate learning from your experience if you have stayed at a monastery or B& B in Assisi
We loved Hotel Umbra in Assisi and would stay there again. It has the feel of a B&B, has a great breakfast, and the roof top terrace overlooks a convent surrounded by a stone wall. The convent possibly has some rooms for guests-you would have to Google for information.
There is an excellent guest house operated by American nuns - Franciscan Sisters of Atonement - called St. Anthony's It is located right next to St. Clare Basilica . There are beautiful views across the Umbrian countryside and magnificent sunsets. The rooms are air conditioned and very clean, good breakfasts and they will pack you a lunch if you order ahead. email email@example.com
Here is the website for St. Anthony's Guest House http://www.prounione.urbe.it/fra-fri/e_friars-stanthony.html
We've always enjoyed La Pallotta in Assisi.