Assuming your print bed level is close but not quite, after the first few layers, it should now longer matter.  The first layer or two will vary in thickness due to the bed not being level, but all subsequent deposits will be level after that.  So the top of each subsequent layer will be at a slight angle with respect to the print bed, but will be level with respect to the print head. 

The image below is an exagerration, but it conveys the idea.

The only real problem would be the extruded plastic not sticking to the bed properly in the areas where the print bed is to low.