not only does it help, but it is required. your CPU will likely overheat without it. thermal compund comes is different formulas (the best one is Arctic Silver 5), heatsinks often come with thermal compound already applied or they put thermal "tape" on, but it is best to remove it and put some AS5 on instead for maximum heat dissipation.
most modern CPUs have a metal heatspreader over the CPU die, in this case you want to spread a very thin layer over the whole thing. if its an older CPU or a mobile CPU with an exposed die, then you want to put a very thin layer just on the die itself and not on the PCB. in either case it is important that you do not touch it with your bare skin. you do not want the oils from your skin or any other contaminents to get into the compound. personally i use a single edge razor blade (brand new and wrapped of course), but a clean plastic bag over your finger will do as well.
it transfers heat better as after it cures, but it loses it thermal conductivity over time and should be reapplied after a year or two.
you dont scrub it, you gently rub it off with isopropyl alcohol (91% is best, but 70% will do)
