Given how the ACX works is it better to have a side fan as an intake fan or exhaust fan? It is standard practice to setup you want it to be an intake to blow cool air down on the cards for the cards to suck in and blow out, but I was just wondering if it would be any different with these twin fan / vent to case designs. 

I am not extremely experienced with this topic, but I do run dual cards with ACX and *SEEM* to get slightly lower temps by making both side fans intakes. I think it goes with positive pressure keeping things slightly cooler and working better, but not entirely sure.

I would say it would be best to have it as exaust since the ACX fans blow the hot air out toward the side door of the case. I am not 100% sure since I have not tested it, just going by observations. Just be sure to have enough intake fans though to keep positive pressure within the case. The best thing to do to be sure is to run an extended benchmark with each configuration to see which works best.

I have ACX and as long as you have good airflow it doesn't matter. The typical front in, side in, lower case in AND rear out upper case out... The worst thing that killed my temps with ACX was trying to run SLI acx... What a joke that was. 

Well how about this, you set up a temp monitor and loop the haven benchmark. Then flip them and test again, after all how hard it is to flip the side fan around. There are arguments for both configs and from case to case things are different. It looks like the power supply will be right below the video cards, does the power supply have a fan on the top that's sucking hot air from the video cards out the back of the case so a intake next to the card would help more then a second exhaust? Time for experimental science!!! 

My HAF XB EVO is a different kind of case and after try the fan both ways gpu temps are a world better as an exhaust. I suggest to try it both ways an use something like HWMonitor for conformation on which works better for you.