The factory cooler in the radiator would be considered a coolant/trans fluid heat exchanger and the aftermarket one a air/trans fluid heat exchanger. The medium doing the cooling comes first IIRC.
And you have it backwards. The Flex-a-lite aftermarket cooler should come FIRST inline, before the stock radiator, not after. The reason for this is that it's possible to make the trans fluid too cold to do it's job and it can cause problems with your transmission.
The way you have it right now the HOT(about 250-275 degrees) fluid comes out of the transmission, enters the radiator(causing your coolant to heat up and making it harder for the radiator to do it's main job cooling the coolant). It comes out of the radiator WARM (say 10 or 20 degrees above your thermostat temp) and enters your aftermarket cooler. It then comes out of that COLD (trans fluid works best around 200 degrees I believe) and proceeds to FUBAR your transmission.
If you put it before the radiator, the aftermarket cooler does most of the cooling causing less of a burdon on the radiator(making it cool the coolant better) And if the aftermarket cooler happens to make the coolant TOO cold the radiator will warm it back up closer to it's happy temp. When this happens your trans fluid actually helps to cool your coolant, making the radiators job even easier.
Hope this wasn't too long winded or confusing. HAPPY COOLING!