The configuration file used for FCKeditor is determined by this Web.config setting:
<add key="FCKeditor:CustomConfigPath" value="~/ClientScript/mojofckconfig.js" />
You should make a copy of mojofckconfig.js with a new name and set it to the new name in Web.config
Then look for the toolbar named "Full" inside that file and add Templates as an item in that toolbar. mojoPortal does assign specific toolbars so you have to edit the one name Full rather than create a new custom one.
Hope it helps,
Joe