First, list the non-disabled plist items with
python list.py
Second, I recommend initializing a git repo in the folder of whichever plists you are going to modify,
cd ~/Library/LaunchAgents
git init
git add .
git commit -m "Initial import of plist files"
Third, go through and disable whichever plist files by copying and pasting the complete path form the list output:
python disable.py /Users/username/Library/LaunchAgents/com.valvesoftware.steamclean.plist
This command will only modify the plist file that is listed.
Finally, I commit the changes to plist in git. This will help detect when new programs modify the launchd configuration.