Hey Mark, I don't think that you need to edit any .ini files.
Just use the MameWAH Layout Designer (should be in your Mamewah directory) to edit the "layout.lay". Edit your layouts so that the size is 640x288 (do this from the menu, Background -> size -> 640 -> 288). This is how Mamewah determines the res to use for each emulator.
For Layout.lay, MameWAH 1.62+ first looks for this file in your config directories (eg mamewah\config\mame, mamewah\config\daphne), and after that in the mamewah\config directory.
You'll either need to use the default Mamewah layout (simple enough), which doesn't have a background image, or make up some 640x288 background images for your emulators (more work than it sounds!). Use the same resolution for all your emulators, it will ease the pain later.
cheers, zeb