Personally, I'm a fan of using 1:1 OS/game settings (6/11 in windows) and setting mouse CPI to what I'm comfortable with (1200 on my current mouse). I imagine this is what most others do, but as long as you keep OS/game settings ≤1:1 you shouldn't run into pixel skipping associated with it.
This is the right thing to do. Never slow down your mouse with OS settings, just leave the OS setting at the very center 6/11 setting, disable enhanced motion, and possibly run a registry edit that further wipes out accel if necessary. Then use your mouse DPI (or CPI) to choose a setting that feels comfortable.
Now technically, when you get inside a game itself, if that game uses mouse looking 100% of the time like in an FPS, it may benefit you to lower the mouselook sensitivity and crank up your mouse's DPI. This can give you finer motion control.