First, make sure you have completed enough challenges in previous playthroughs to have 2X multiplier. Now, focus on hitting headshots and hiding bodies. The headshots and hiding the bodies will help with getting enough points. Hiding the bodies is also required for a Silent Assassin run. You can use your shock wave bullets to push bodies into hiding places if you ever miss.
*MrFreeze2244's video is very useful, helped me get up to level 20 really quickly.