If ALL of your intake fans have a decent quality dust filter in fronts of them then you definitely want slightly positive case pressure. As in, you want slightly more intake than exhaust fans (assuming all your fans are the same). Having more exhaust fans (negative pressure) will result in air being drawn into the case from places other than the dust filters, resulting in a lot more dust inside the case.
Some cheaper cases don't have dust filers on the intake anyway, making it irrelevant. Also, in my experience, even with positive pressure and dust filters you'll still need to dust your PC from time to time anyway. So in the end of the day it doesn't really make that much difference.
RE Thermal paste, usually you put a spot in the...