Are we talking Intel or AMD chip here? AMD coolers need a lot of brute force to get into place. (I use a large flat-head screwdriver on the clip).
Removing and reseating the cooler too much wont do the thermal paste any good, it will end up with air pockets that can cause hotspots and raise the temperature for some cores. If you have to reseat it, give it a wiggle in place before clamping it down.