On an AOD, the fluid leaves the radiator at the bottom IIRC. You can check this. Disconnect the line and put a barbed fitting and hose from the radator (side of the disconnected fitting) to a bucket. Crank the car and ensure that fluid comes out of the radiator. If it comes out of the hard trans line, that's the wrong line.
Lang, you might want to put the filter before the cooler if it's a new cooler. If it's a used cooler, put the filter after the cooler (before it goes back into the trans). YOu can do all of this without ever touching the or cutting the OEM hard lines.