Whether you get 2S1P or 2S2P, depends on what configuration gives you what you are looking for in terms of discharge rates and capacity.

If you go with the 5000mAh cells and get the 5000mAh packs, then each pack will be 2S1P. If you want to go with more capacity, then you'll probably go to the 8000mAh capacity packs which are made up of 4000mAh cells in a 2S2P configuration (two pairs of parallel cells in series).

With the Quark, many have told me that a heatsink will suffice, although some do use the fans. Ask Mike how he runs his.