I'm building a new system that will include two overclocked Gigabyte GTX 560 TI GPUs in SLI and an overclocked i5 2500K coupled with a CM 212+ CPU fan. I'm using a CM 690 II Advanced case but a bit worried the stock fan setup won't be enough. I was thinking of adding an additional 140mm side panel intake fan coupled with a 140mm top exhaust fan. Will that do the trick or should I add a 120mm HDD mounted fan as well? Also, with two 140mm top exhaust fans would it be better to mount the CM 212+ horizontally to exhaust upwards towards the top of the case or keep it in the standard vertical orientation to exhaust towards the rear?
that case should accommodate 2 560s you should be fine as long as you remember to keep a good gap in between gpus. coming from my hafx and v6gt, either horizontal or vertical is fine, and wont matter much, although you'd want to have incidental airflow coming from the heatsink fan hitting the VRM sinks on the board, if any.
EDIT: side panel fan didn't help much with my crossfire temps many moons ago, but an additional top mounted fan exhaust should help with convection when things get hot. reference video cards will help keeping the case temperatures too because they exhaust hot air directly out of the case instead of dumping most of it inside especially if you have 2 of them running.
Best way to mount CPU cooler is almost always with it exhausting out of the rear of the case, not the roof.
With the 212+ I think your going to struggle to fit side fans on the case due to the height of the cooler, and the width of the case. Buying low-profile fans if anything might help get around this. Otherwise i recommend buying side fans AFTER you build the rest, just to make sure you have enough space to fit everything in.
One front intake, one/two roof exhaust, one rear exhaust is usually plenty for cooling. Any more than that other than maybe a side intake (if it will fit) to help cool SLI graphics wont really make any more difference. Your always fighting with ambient air temp anyway.