You can set how containers (both normal notes and agents) sort their children by visiting the Sort tab of the Action inspector:
You can choose what attribute to sort by — $Name, $Text, or what have you. I believe lexical (i.e., alphabetical) sorting is the default (or perhaps the only option?) for String attributes.
More info in the indefatigable aTbRef: http://www.acrobatfaq.com/atbref7/index/Windows/Inspector/ActionInspector/Sorttab.html