The conversion "programs" are contained in the files found in the BACKEND directory called CV_SVxxxxx.SQL where xxxxx is the conversion area being considered (e.g. cv_svpersonals.sql is the program for converting personals).
It is recommended that you have a separate and distinct directory for your conversion activities and that you should have in this directory your CTL (SQL Loader control) files, your source data and any scripts that you are writing to deal with conversion. In this directory, you should copy your modified CV_SVxxxx files as well.
This directory should also be the "start in" or working directory for your SQL icon used to launch SQL*Plus for your conversion activities. This will ensure that any scripts you run, or any re-application of CV_SVxxx scripts will pick up the correct versions.