If you navigate to Manager Home > Configuration > Items, you'll see the item tree.
Expand the department you wish to sort, and expand the category within it to see the items.
Select an item and use the "Move Up" or "Move Down" buttons to change the order within the category.
You can also do this with categories themselves, to change the order of modifier categories when editing an item.
Be sure to press SAVE at the bottom of the screen to save your changes.
Changes made on this screen may not automatically update to Thrive Online, so edit any item and save to trigger an update, or go to your Thrive Online Admin > Locations screen to import your menu.