After the initial menu import, performing a sync will add new items to your Item Library, but will not be automatically added to your online menu. All new items will appear in the New Items from the POS section of the menu and in the Item Library.
To place new items in the correct section:
Open your menu
Check that the new item is in the New Items from the POS section
Select the Show Items under the Item Library
Open the section you want to move the item to
Search for the item in the Library list (Ctrl F) to do a search
Locate the item and click the arrow next to the item to move to the section you have open