The BPPC has a cooler very similar to modern day GPU heatsinks. There is a sealed cover over the entire heatsink which directs airflow. The fan is on the underside of the board but connected to the output of the cooler.
Look at this photo where the heatsink has been removed
http://amigahardware.mariomisic.de/download_photos/blizzppc040_front_big.jpgThe heatsink touches the CPU, has a network of channels that lead to that big hole. That is where the fan goes on the other side of the board.
To fit the new fan I take it you had to remove the board from the A1200 motherboard??
Check that the connection between the A1200 and BPPC is good.
Check that non of the removable components (crystals etc.) have come loose.