Just look at the model from a top-down view and use the grid lines to figure out where the spaces are. If it's not an even size, you might have to shift it over by .5 to get it to line up properly. You can also figure out the cell map before you even make the model if you draw out your concept from a top-down view. I've found that saves a bit of trouble because I have a reference for where all the openings and doorways go, and already know the cell map.
How about making a big castle that can hold units inside? with cell map of course
I didn't understand what you meant at first, but now I think I do and it sounds kinda interesting. It would lack a lot of the capabilities that people want from walls, but it might be a good starting point for a tower/keep. In that case, there would just have to be something telling them that at the 0 spots in the cell map, they should be up off the ground.