personally, and this is totally personal, i don't partition but run 2hdds, on that has the os/apps and another that is for storage, but i don't reinstall and reformat very often (been nearly 1.7ys). if you do, then you may consider partitioning.
as far as the room and temps, take temp readings, then take off the side panel for a day and use the computer like your normally would, if the temps are pretty close - a couple of Cs then your are doing fine