I'd say you should experiment with [Slic3r][1]

it can manage extrusion in very sophisticated way

it can overextrude if you need a line wider than actual nozzle size
as same as it can underextrude if needed
it can even change extrusion continuously while extruding one line

here are simple examples
[![enter image description here][2]][2]

i use [mattercontrol][3] and slic3r as slicing engine


  [1]: http://slic3r.org/
  [2]: https://i.sstatic.net/Y9ARQ.png
  [3]: http://www.mattercontrol.com/