There is no perfect layout as cases very so much, and some cheaper cases don't really pay attention to good air flow. Sometimes its just a little trial and error to see what gives the best temperatures. As others have said, top and back are most often best as exhaust. I have heard of side fans working best as intake or output depending on the computer (See which improves your temps).
Are you using the pre existing holes in your case or cutting holes for new fans? You want all you rear and top factory fan mounts filled with fans. If say for instance, you have 2 rear fan mounts but only 1 fan, it takes a lot less pressure for the fan to draw air in an empty hole and right back out the other with the fan, than it does to draw air through the entire case and through vents etc. If you cannot fill all the fan mounts, block the unused exhaust ones on the back/top as you don't want them to inadvertently become an intake (mounting what fans you do have in the highest location). Fans are not that expensive if you get them on sale. I would strongly suggest filling all exhaust holes with fans.
Check your hard drive temps through software, or just run/use the computer for a while, then take the side off and see if they are hot. If they are a little warm, fine. If they are hot to the touch, I would try to improve cooling. If you have hard drive cage fan mounts, use them. If not, look where you have vents, and selectively, partially block them to create negative pleasure to draw air over your hard drives). I other words, if you have vents in the bottom floor of your computer, you could block them across the middle but leave them open at the front and back (it really depends on where they are located and how big they are). That way you still get air flow through the vent, but it is reduced, causing negative pressure (a vacuum), that will draw air in from other spots like the hard drives.