If your heatsink's fan is mounted blowing on the heatsink, blowing on the whole hsf will most definitely be the way to go, with a sucking heatsink fan, you would have to try it out, but imho blowing on the hsf is always better!
I think it's better to have them blow in and if you have room at the top...make it an exhaust. And if you have even more fans...add 2 to the back. Here's my set up. 1 92mm fan on the left side (intake), 2 80mm in the front (intake), 2 80mm in the back (exhaust), 1 92mm on top (exhaust).
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