I'm not fully sure what you want. But, all the settings for the actual map size is done inside the map maker.
The size of the heightmap image is just how many pixels the picture will be that the map use. Not the actual size that you run around in.
As ruby mentioned you should focus on the world tab inside the map maker.
In here you set the width, and the height in the 2 fields given for it there.
It's pretty much self explained.
The height size you can use is pretty much up to yourself.
If you set it to a high value such as 1000 in height. The black on the heightmap picture will be the absolute bottom, and the absoluute white colour can be as high as a mountain. But if you set the height value to something like 300, STILL using the same heightmap picture, the absolute white could just be more like a bump or hill on the ground instead.
Play around with these numbers and set what you think looks good or is wanted.
As fast as you press test, or go back to the map maker menu, the heightmap should automaticly load the changes that has been made, so no need to turn off the game either.