Well, as you are searching a free software, hotkeynet might be a solution for you, even if you don't want to pass keys.
Hotkeynet can be found at www.hotkeynet.com .
A simple script to do what you described would look like:

Code:
//-----------------------------------------------------------
// SUBROUTINE TO LAUNCH AND RENAME A COPY OF WOW.
//-----------------------------------------------------------
<Command LaunchAndRename>
   <SendPC %1%>
  <Run %2%>
  <RenameTargetWin %3%>
  <RemoveWinFrame>
  
//-----------------------------------------------------------
// SUBROUTINE TO Position Windows 
//-----------------------------------------------------------
<Command ResizeAndPosition>
   <SendPC Local>
	  <SendWin %1%>
     	       <SetWinSize 1280 512>
     	          <SetWinPos 0 0>
	  <SendWinM %2%>
     	      <SetWinSize 1280 512>
     	          <SetWinPos 0 512>     
     
//-----------------------------------------------------------
// HOTKEY TO LAUNCH AND RENAME YOUR WOW WINDOWS 
// Please configure the Path and processor afinitys correctly
//-----------------------------------------------------------
<Hotkey Alt Ctrl L>
<LaunchAndRename Local "C:\temp\multi\w1\wow.exe" WoW1>
<LaunchAndRename Local "C:\temp\multi\w2\wow.exe" WoW2>
<ResizeAndPosition WoW1 WoW2>
with this you can start the two wows with a press of 'ctrl + alt + L' and the ResizeAndPosition-command resizes them then.
To get this working you need to use the correct path in the LaunchAndRename-command and perhaps customize the window-positions and sizes.
More detailed infos how to do this can be found in the here: Hotkeynet Guide: Resize and Position

If you need anymore help, simply ask here or on the hotkeynet-site.