By default, Application Wizard sorts applications and AppleScripts alphabetically within groups, but you can turn off automatic sorting and manually rearrange applications and AppleScripts as you like.
Open the Application Wizard pane in System Preferences and click Groups.
If you want to arrange groups and applications or AppleScripts manually, choose Manual from the Sorting section of the Action pop-up menu (looks like a gear).
If you want to arrange applications and AppleScripts manually, but keep groups sorted alphabetically, choose Groups from the Sorting section of the Action pop-up menu.
Drag applications and AppleScripts in the list to rearrange them.
No matter whether you keep applications and AppleScripts arranged or not, you can move or copy them within groups.
Select one or more applications or AppleScripts in the list.
To select items that are next to each other (contiguous) in the list, press the Shift key and then click the first and last item; to select items that are not next to each other in the list, press the Command key and then click each item.
To move the items, drag them to the other group.
To copy the items, hold down the Option key and drag them to the other group.