Here is the HotKeyNet script I came up with to arrange the windows

Code:
//-----------------------------------------------------------
// SUBROUTINE TO LAUNCH AND RENAME A COPY OF WOW.
//-----------------------------------------------------------
<Command LaunchAndRename>
   <SendPC %1%> 
      <Run "C:\Users\Public\Games\World of Warcraft\WoW.exe">
        <RenameTargetWin %2%>
//-----------------------------------------------------------
// HOTKEY TO LAUNCH AND RENAME
//-----------------------------------------------------------
<Hotkey ScrollLockOn Alt Ctrl L>
    <LaunchAndRename Local WoW1>
    <TargetWin WoW1>
        <SetWinRect 0 0 965 795>
    <LaunchAndRename Local WoW2>
    <TargetWin WoW2>
        <SetWinRect 0 795 965 795>
    <LaunchAndRename Local WoW3>
    <TargetWin WoW3>
        <SetWinRect 965 0 795 660>
    <LaunchAndRename Local WoW4>
    <TargetWin WoW4>
        <SetWinRect 1760 0 795 660>
    <LaunchAndRename Local WoW5>
    <TargetWin WoW5>
        <SetWinRect 965 660 1135 930>
The next step is to get the windows to swap around using some sort of key press combination