There are alot of different ways this could be done.
Off the top of my head...
Create your folders
Then to present random messages from that folder, build an array that contains the message file names.
At random pick one of the messages
Then using @Site (assuming that you have AD and there are two seperate sites) put the contents of the selected message into a messagebox.

Here is a logic flow, not by any means a working script
Code:

$Messages = DirPlus("\\server\messages","*.txt")
$Count = Ubound($Messages)
Select
  Case @Site = "Site1"
    $File = Rnd($Count)
    $ = MessageBox($Messages[$File],"MOTD")
  Case @Site = "Site2"
    $File = Rnd($Count)
    $ = MessageBox($Messages[$File],"MOTD")
  Case1
    $ = MessageBox("An error was encountered please contact the help desk", "Warning")
EndSelect