I would put it so it blows on the AGP, because if you get a new motherboard, you will be stuck with a fan that is blowing on nothing (possibly), while if you put it in the AGP area, it will always be there. Your graphics cards usually get pretty hot too. Always good to get some more air in there. Make sure you have as much blowing out as you do in though.
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Off the record, on the q.t., and very hush-hush.
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