I have been doing Chilean family work for years, but resources are limited.
I have had very good results with the records now in FamilySearch.org. They have many actual images of the Chile, Civil Registration, 1885-1903, but hardly any are indexed, so you will have know the location and go image by image. They have some indexed Church records. This will be your best source in my opinion.
Also try the following:
• Instituto Chileno de Investigaciones Genealógicas: http://www.genealogia.cl/