Well you should use comicrn /completed download handling (not both obviously), as you'll get better results with either.
Completed Download Handling (CDH) is just a checkbox on the nzbget section within Mylar. Enable it, and that's it.
Both comicrn and CDH have the benefit of not having to specify whee the final comic is to be post-processed from as the client tells both exactly where it is.
You also have to make sure that if your using a newer version of autoProcessComics.py, that you autoProcessComics.cfg is also the correct version (meaning aPC 2.x has apikey, 1.x has user/pass) and that it contains the relevant information.
Post any problems / bugs / issues that are Mylar-related in here.