For Magnefine filter installation instructions, see:
Magnefine--Magnefine Filter Installation Instructions
Since your vehicle has had transmission problems, the filter should be installed in the return line from the cooler to the transmission. The return line is the metal line running to the BACK of the transmission. This metal line hooks to a rubber hose that runs around the right side of the radiator to the transmission cooler. Install the filter in this rubber line.
The filter is directional, so make sure that the filter is installed with the arrow on the side of the filter pointed in the right direction (in this case, toward the transmission).