Hi,
Yes, mojoportal is using the mojofckconfig.js file. However I don't recommend customizing that file directly. Instead, copy it and rename it and then change this setting to the new file. You will find this in Web.config but ideally uoi will override it in user.config
<add key="FCKeditor:CustomConfigPath" value="~/ClientScript/mojofckconfig.js" />
If you were to just customize mojofckconfig.js directly, you would likely lose your customizations next time you upgrade because the new file would replace the old one. By using your wown named file you can avoid this.
One other thing to be aware of is mojoportal's .NET wrapper around the FCKeditor needs the toolbar names to be as they are in mojofckconfig.js. It doesn't allow you to add new arbitrary named toolbars, but you can customize the exsiting named tool bars.
Hope it helps,
Joe