In order to sync the tracking number on the All Orders Ship Doc to the Invoice in QuickBooks please do the following.
1. In QuickBooks create a Customer custom field called Tracking No.
2. In All Orders, make sure you are logged as Admin and do a Sync.
3. In All Orders go into Company Preferences - QuickBooks Synchronization then click the SO/Shipping tab.
4. Press the little swirl icon and then select the custom field you created in #1 above where it says Tracking #. Then click OK to exit the Preference.
5. When doing a Ship Doc put the tracking number in the Ship Doc Reference box and sync as normal.