HKN is a good solution, if you want to go with it.
IS Boxer is more powerful and flexible, if you think it is worth the subscription vs HKN being free.



As far as the Window Layout...

There's the size that each of the regions is rendered at, which is the game resolution.
This can be whatever you want, subject to what your system can handle.

Then there is the physical window size, on your monitor.
I have five regions, each rendered at 1680x1050, but four fit across the bottom of my 2560x1600 monitor.
With a larger region along the top, which warcraft thinks is also 1680x1050 even though it stretches across the full 2560 width.

The size the windows are rendered at, is not the size they are displayed at within your Window Layout.