It seems to me that Maximizer could do this since it recognizes margins (regardless of what your screensize/resolution is) in order of
Upper Margin, Lower Margin, Left Margin, Right Margin
0 meaning that the screen is maxed out towards that margin.

REM batch file to launch 3 screens on 2 monitors
REM Left monitor
c:\wow1\maximizer.exe --margin 0,0,0,1440
REM Upper of right mon
c:\wow2\maximizer.exe --margin 0,512,1440,0
REM Lower of right mon
c:\wow3\maximizer.exe --margin 512,0,0,1440

Although I'm not sure if that would actually work, it would be easier if the main monitor would be a [value]*1024 resolution.. and don't forget that splitting the 2nd monitor will stretch the windows out :

http://www.dual-boxing.com/forums2/viewtopic.php?t=1767

There's some hints in this thread as well as how to set game resolution in the config.wtf file:

Go to your WTF folder, and as soon as you open it, there will be a Config file in there, open it with notepad, and edit the SET gxResolution.

So the two top windows have:
SET gxResolution "840x480"
and the bottom (main window) one has:
SET gxResolution "1680x570"

Just don't change any video settings in-game, or it'll reset the resolution and you have to re-edit the config.wtf files.
in your case it would be 1440*900 in your main and 1280*512 for the other 2..