Hi - thanks for posting in my thread. I cant post images right now but to explain the parts you asked about:
The front fans: They push air through the channels that the HDD's sit in. Each channel is separate from the other and the air from this section is exhausted out the top follow the lines of the channel with your eye and they go up wards to top of case - hot air exits here. If you go to page one of this thread, you'll see the original idea and it is clearer I think in this image. hope that helps.
Cooling for motherboard area: Out of the channels for the HDD's, the one at the very bottom, has no HDD in it, it is reserved for the 'main chamber' or area-where-cpu-gpu-motherboard is. To explain how this works I need to finish an air-flow illustration I'm working on, but I'll try here - There will also be 2 180mm fans in the main chamber, they are situation on the right wall of the chamber which is the back of the HDD channel system (they are not in the posted renders - top secret stuff ) and they suck air from the bottom channel, which is the one with the holes in the side, this channel has the largest surface area as it wraps around the whole chassis so there is no bottle-neck effect on air coming in. The air from the main chamber will quite boringly just leave through a bunch of holes (or maybe I can make it evaporate with lasers??). it is also assisted by air blow through bottom channel by the front bottom fan.
PSU's tend to have their own built in fan system so all Im doing in that area is closing it off from main chamber to stop it affecting the ambient temp too much. The psu fans tend to suck in from bottom or top and blow out the back.
So to re-iterate: The air from the main chamber will blow from right to left/top, from 2 180mm fans, each covering a half of the MB. The air for these fans comes from directly behind them, where there will be a cut-away where air will travel from the bottom / back channel from the HDD system, and the air for this comes from all along the side of that particular channel (the only one that is vented along the sides, front and top of case).
At the moment we are all moving to the physical modeling phase so we probably wont be posting on here as much, the project ends soon (17th). Personally I am going to get the model out of the way as soon as possible because in my particular situation it will explain very little about my design - it's essentially a traditional chassis shape, however it's got to be done....