Here is the reply from Kontera support which should answer everyones question on How to..
Quote:
In vBulletin, if you want the links to appear in posted messages, you need to add the Kontera code before the BODY and HTML end tags in two
templates: SHOWTHREAD and SHOWTHREAD_SHOWPOST
You can find these templates in the Admin CP by going to the Styles & Templates area, choosing the Search in Templates option, and then searching for SHOWTHREAD and SHOWTHREAD_SHOWPOST. Choose the "Search Titles Only" option (it's a radio box).
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I hope that helps anyone else as this is the proper location for the code to ONLY show up in thread posts and not site text or header titles etc.. I've tested it and it works perfect!
FYI: the code is all the way to the bottom of those templates above the /body coding.