All the JAM8 windows have a parameter called 'Mode' which allows you to tell the object how to interpret your width and height dimensions. (Then there's schematic mode which draws a glass box. More of a bar stunt than a feature, but it does work.)
The default is for the windows to treat the height and width as the frame size, the outside measurement of the unit. I chose this behavior because it is the most objective overall measurement for a window, when you consider different manufacturers. The other option is 'Jamb', which treats the height and width as the inside dimension of the frame instead of the outside. When measuring an existing window, this is the measurement you'll have.
Both the frame and jamb modes place the window so that the INSIDE of the head is at the head height as given in the settings box, which is the sill added to the height parameter. That is, switching from frame to jamb DOES NOT move the window in Z. The head height in the settings box always reflects the finish head height (above the subfloor, of course).
Reread the preceding paragraph several times.
Window companies are notoriously idiosyncratic about sizes, dimensions, standards, and terminology, to the point that the statement, "I want a 2-8 double-hung" is almost meaningless. Weathershield, for example, refers to its frame size as 'Jamb-to-Jamb', where normal people would think that meant the inside jamb dimension. Not helpful.
You have to develop a knowledge of what the different manufacturers mean by their terms. The only way to do this is to study their details and find the relationships among the various size definitions.
One of my more ambitious goals for the next version of the windows is to teach them the technical differences among the manufacturers, but it might be more trouble than it's worth. In the meantime, as usual, there is no substitute for understanding what you're doing. You might have to put in counterintuitive values to get the windows to behave correctly in a given application. I do it all the time.