The only place you should place thermal paste is the GPU's die(a pea sized amount) and let the cooling plate spread the paste across when you tighten the cooling assembly. You can't substitute thermal pads with thermal pads though. You could look into thermal putty instead of thermal pads but the old school way of doing things is high quality thermal paste on the GPU die and high quality thermal pads on the VRMs and everything else that should make contact with the heatsink.
Got a link to the GPU's in question? You could try undervolting to help alleviate your overheating issue, if your case has ample airflow. Speaking of which what is the make and model of you case?