Whether you use height or width is arbitrary. It's used to set up a size for Virtual Pixels that split the screen into that many parts. If the virtual pixel height (UIRoot's activeheight) is the same as Screen.height, then Screen.width will also correspond to the coordinate system made by UIRoot (localPositions).
If you mess around with the manualHeight, then you need to calculate the corresponding width based on the aspect between height/width.
Externally in your own script, you can easily do these calculations and feed a manual height into UIRoot if you want to change it at runtime.