I believe he was convicted on the testimony of his own brother, who was on the boat and said that after the cooler floated, Capano shot it full of wholes to get it to sink, but it fell open and the brother saw a human foot going down into the water.
In an even stranger twist, they were able to match blood from Capano's house to Fahey's blood because she had donated blood a few days before her murder--they had to literally stop a ship heading to Europe with the plasma on board.
http://www.crimelibrary.com/classics5/capano/3.htm
is the link to the cooler murder guy.
Seeyabye