Hi Barbara,
Two nights is exactly right. Assisi, a bit like Capri or Positano, is a completely different place once the day-trippers leave (much quieter and more easily navigated), and if you get to the Basilica of St Francis early in the morning you can have it almost to yourself. For the luggage, the easiest answer is to stay inside the old town walls. Every hotel there will happily hold your bags if you arrive before check-in, so you can drop everything and do the walk unencumbered.
I’d look for somewhere in the middle or upper part of town, around Piazza del Comune or Santa Chiara. Rick’s walk starts at the top (Piazza Matteotti) and works downhill to the Basilica, so a central hotel puts you on or near the route. Your day could look like this: Line C bus from the station, hop off at the stop nearest your hotel, drop your bags, then carry on up to Piazza Matteotti (by bus or a short, steep walk) and stroll down through town at your own pace.
One small tip: the streets are steep and cobbled, so minimal luggage is essential. Wheeling a small case from the bus stop to a central hotel is fine, but I’d avoid anywhere with a long uphill walk from the nearest stop.
Enjoy it. It’s one of my favourite places in Italy.
Nesse