Yes.....the upper line is the input to the radiator cooler from the tranny
The lower hose is the out from the radiator cooler to the input on the aux tranny cooler.
The output from the tranny cooler then goes back to the tranny
Same at the cooler (upper is in, lower is out)
An easy way to remember this is, think GRAVITY is your friend.
Fluid enters at the top and leaves at the bottom, this helps the pump push the fluid through.
When I converted my truck to auto I could never remember which was which and I had to keep looking at a friends EX.
I replaced the metal lines with high temp high pressure tranny rubber lines. I used a single flare tool and hose clamps, cut the stock metal lines about 4" after they leave the tranny and cooler. Works GREAT!!!
Hey while you are at it think about installing a larger tranny cooler, best insurance you can get!