The third-party tracking code needs to be placed in an embed block on all master layouts requiring tracking. To add the tracking code to the master layout, go to:

1. Navigate to onMessage > Website > select appropriate website.
2. Click the Master Layouts tab and edit one of the master layouts.
3. Drag the embed widget onto the page. 
4. Click the settings cog wheel and paste the third-party code. Remember to apply these changes.

Do some testing to make sure the tracking code is firing when a user visits the page. Remember to add the code to every master layout that needs to track the site analytics. 

Note: This is different than adding Google Analytics tracking, which can be added in the Settings for the site.