Depending on your design. If level is small, means like a standard fps shooter or L4D2 map (still not really big levels) for example, you can place trees manually for better design effect. But standard way is use foliage paint, then edit it manually (you can select and remove single foliage, tree, rock etc). Here also other method with auto foliage painting, but in my opinion is better paint it manually even on large world (I work on open world game and this way is ok) then edit.
Finally, you can mix both method - paint manually in non key areas and place meshes in important for design places, for example around buildings etc.