OK, I’ve not got much experience with it, as you could probably tell. =)
If it’s a text file, I like to manipulate them with perl:
Replace abc with def:
perl -i~ -pe ‘s/abc/def/g’ filename
If its a plist, which I think it is (not sure, is it the /Library/Preferences/com.apple.alf.plist?)
Then I would try to use PlistBuddy or defaults to add additional exceptions.
Hope that helps!