The best way to to cool a GPU is with a side fan, however, it will increase the noise over a solid side panel with the moduvent in place. Second choice would probably be to remove the center drive bay and put an air flow (versus static pressure) fan blowing on the GPU, but I don't it would add much if you already had a side fan in place.
https://www.pugetsystems.com/labs/articles/Side-Panel-Fans-Are-They-Worth-It-102/
http://www.hardwaresecrets.com/which-is-the-best-place-to-install-a-case-fan-part-2/