Exactly. The other configuration (parallel to the mainboard) has proven to be much less effective (at least in my case... And in my case he he ;-) )
I probably should have mentioned that along with the fan blowing on the top of the cards, I have a 120mm high pressure fan blowing air out of the front of the case. I believe that makes the difference. Tons of heat comes off the rear of the cards and it gets pulled out by that other fan.