Sorting is done on the Theme: Kitchen tab of the same Configuration page:

1. In Show on Header Menu, tick the modules that should appear under the site's Order menu - the list includes Packs, By Pounds, Choose Subscriptions, Choose Meals On Subscriptions, A la cart, Custom Meals (CMB), Giftcards, Extras, Products, Real Time Ordering, Catering, Wholesale and Grab&Go.
2. Give each listed module a number in its matching Menu Order: ... field (Menu Order: Packs, Menu Order: A la cart, Menu Order: CMB, Menu Order: Grab&Go, etc.). A few modules on the list (Catering, Products, Realtime, and the base Wholesale entry) do not have their own Menu Order row in the current version.

Modules are listed from the lowest number to the highest; modules with the same number are then sorted alphabetically by their Title. The label of the drop-down itself (Order) is changed under Theme: Navigation > Name: Order.

If you've added extra A la Carte storefronts (see the next question), each one gets its own Menu Order: <option name> row here too.