You need to do both - set maximizer.ini margins AND the in-game resolution in the config.wtf file. WoW Maxmizer just maximizes a window (removes title bars & borders) in a given area of the monitor. This means that it'll stretch the current resolution to fit the window, without retaining the correct aspect ratio (proportions). You need to edit the config.wtf file to let the game display propertly proportioned UI and graphics within that given window.

As an example, I tried running all 5 windows on my 1920x1200 monitor using 5 stacked windows at 1920x240. The perspective looked perfect - nothing was squished or distorted, but it just wan't very playable with the lack of view area for my main character, and opening bags was a nightmare. There was simply too much wasted space on the sides of the characters. I then tried this format:
2 top windows at 860x600 each.
3 bottom windows at 640x600 each.
Again, perspective was perfect, but I just didn't feel like there was enough room available on my main character. That's when I decided to bite the bullet and just use dual-view on my two monitors.

If you try to fit two WoW windows using maximizer in one 1280x1024 monitor without changing the config.wtf file from one of the standard resolutions, the game will distort as it attempts to fit a 4:3 or 16:10 resolution into a 2:3 or 8:3 window. Changing the config.wtf to the correct (exact window size) resolution will prevent this distortion.