Just adding two mono tracks and assigning L and R to mics doesn't create two recordable tracks. They both will still record on one track.
In audio setup add two mono inputs. Then click the Track tab at the top of the screen, choose 'add tracks for all inputs'. Then delete any input track you do not want such as 'Stereo'. Now when you record it will record each mic separately on different tracks allowing you to mix and add effects independent of the other.