... it converts the mail but places it in my non-viewable cgi-bin. How do I rectify that
That was pointed out in Earl's reply. It is also explained in the "Quick Start" document you told us that you have studied.
and secondly how do I get this process automated?
What do you mean by automated?
You need to spend some time with the documentation and the FAQ in order to understand what MHonArc can do and to set it up properly.
I wrote a help script for MHonArc: http://www.gunnar.cc/mhonarc/mhastart.pl.html Even if it's primarily intended for users that don't have shell access (which you obviously have), it might help you to get started.
-- Gunnar Hjalmarsson Email: http://www.gunnar.cc/cgi-bin/contact.pl