We visited the site in 2015. Many of the churches are quite spread out, and if you really want to see the best of what this site can offer, you’ll need to rent a car. We flew into Puerto Montt, and drove down. There’s been talk of connecting the island to the mainland by bridge for years now, but as far as I’m aware, that’s still not come to fruition, so be prepared to take a ferry.
The churches, like many things Latin America, are outwardly Christian, but with a strong local flavour. There’s a decently well signposted tourist trail, though be prepared for some tricky driving conditions. Not every WHS church is on the trail and not ever church on the trail is WHS, so if your time is limited, I recommend doing a bit of research ahead of travelling.
Castro makes a great central base from which to visit more remote islands. We stayed in a beautiful hostel in a palafito, a local style of stilthouse. The food was also spectacular, and unique to island.
All told, we visited 11 of the 16 churches. My personal favourite was Detif on the island of Lemuy, which is the furthest south, and requires an additional ferry to get too. Lemuy is Chiloe in micro, and an immensely relaxing way to spend half a day. You can visit a majority without leaving Chiloe proper, but I think you miss out on what makes the place special if you don’t get out to one of the smaller islands.
Other stand-out churches include Castro (easily the biggest of the churches), Rillan (with its stunning blue and white colour scheme), Chonchi (attractive astrological map painted on the roof of the church) and Tena (a good drive and close to the water's edge). We had no issues getting into any of the churches, with one even letting you get right up into the rafters.
Make sure to visit the the stunning Chiloé National Park for an amazing unspoiled coastline, and the Islotes de Puñihuil in the north-west for a chance to see wild penguins.
Chiloe is a special corner of the world, and despite the long journey and out of the way nature of the site, it was a proper highlight of all of my travels to Chile.