I know this sounds silly but you want to be blowing air in to the general area of the air intake, but don't put the fan(s) to close to the cards. I found having too much air movement near the graphics cards intake can actually hinder the GPU fans ability to work properly. As I said, do some testing and see what works best in your rig.
As for the power connectors for the fans; either connect them to the motherboard or directly to the PSU. A pic of the internals of your rig might be helpful
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