I currently have the front intake as exhaust to dispel heat from the GFX card, the 2 on the side panel as intake, top front (closest to CD Drive Bay) as intake, and rear top and rear ports as exhaust. The bottom front intake is unused.
Is there any better airflow setup that i can go for? Or is this airflow setup actually hurting my system? Also, how is the dust management?
Probably run two front intakes at about 7V, 1 fan on the side at 7V, and the exhaust at 12V, and leave the top fan mounts clear, it'll allow for natural convention to occur - your components will be cooled, and the hot air will rise through the ceiling & be sucked out the exhaust.
I agree with payturr 95% . Its generally agreed that a more or less uninterupted airflow from( front / low ) to ( rear / high ) gives the best cooling solution . Your card does present a hurdle to this but IMHO you'd do best to follow payturr's advice but I would add exhaust fans in the roof mounts and run them at low voltage .. Best of luck