In October 2017, I made an easy, but long, day trip by bus from Puerto Montt to Castro, probably the best base from which to visit the wooden churches. One of the best wooden churches, the Church of San Francisco, is next to Castro's bus station. I arrived in Castro around 11:30 am, so was able to visit the interior of the church, which on the day of my visit was open from early morning to noon, closed early afternoon, and then reopened in the late afternoon.
Since I only had a few hours to visit several of the shingled churches, I booked a tour with Pehuén Expediciones (http://www.turismopehuen.cl), a local operator that I found while on my way for lunch at one of the restaurants in Castro's palafitos, traditional wooden stilt houses that sit above a tidal flat. There were other operators around the main square, and I expect they can set up similar day trips. I organized a few-hour tour (45,000 Chilean Pesos, approximately US$70) to visit three nearby wooden churches. We first drove around 20 minutes to the farthest church, the Church of Chonchi (I arrived around 2:30 pm and the interior was open). While heading back to Castro, we stopped at the Church of Vilupulli (it was locked, but my guide was able to drive to a local school and return with a neighbor who maintained the key; after our visit, we returned her to the school -- without a guide, I doubt I would have obtained access to the stunning interior). Finally, just outside Castro, we stopped at the Church of Nercón (its interior was open).