Megahalems/Fans setup Questions

Just received Megahalems cpu cooler, and have A few Questions about setting it up.

1. Does it make any difference in which direction they are mounted. I have A Cooler Master Storm Sniper case and would like cpu exhaust to be bolwing out the top 200mm fan insted of the rear 120mm fan(case has side panel 200mm fan). The Prolimatech web site says "direction of heat sink-faces the rear exhaust sustem fan". I think this statement is just for the standard case layout. Opinions?

2. Should I connect the 2 Scythe SY1225SL12SH(12 Volt 0.53 A) directly to the power supply or can I connect them to the motherboard fan headers(ASUS p6t Deluxe V2). Would like to have on the motherboard for speed control.

From research I have done the megahalems will fit into case with side panel fah attached.

I have the lclc cpu cooler now, but my temps have been reaching 90C with Prime 95 with small fft's. i7-920 @ 4.0 1.25 core voltage with ambient temp around 25C.

Any thoughts?

I have a HAF-932 case and intend to mount my Megahalems to exhaust the heat vertically to my 230 mm top fan as you intend to do. Assuming I have the room, I'll be using my Sanyo Denki's 109R1212H1011 120mm x 38mm in a push/pull orientation. So what you're doing seems like a great idea to me.

Since you don't have a hardware fan controller, connecting your fans to the mobo should do nicely for fan control. You want to be able to control their speed, otherwise they'll run at max RPM all the time. The only difference is I'll be using a Lamptron FC-5 to control all my case fans.