Frank, the _cities.ini is a file only used by Terrain Editor (TE).
The in-game terrain engine doesn't use it (you probably know this!). What it's good for is, you create your cities/airfields in TE, and use the flattenning function..
After creating airfields/cities and target areas in TE, you do a "save all" which will update the _cities.ini.... Then you copy over the target area coordinates to your terrain_targets.ini.
I only used it at the beginning of my terrain project. After a year of development, major airfields and cities were put in place, I switched over to manually placing target areas with the HUD DEBUG option (a PITA, but the outcome is, you get much more realistic target areas.. I don't like flatting a hole 4x4km tile space for a city and have it look fake..
The maps are pretty important, and with Wrench's ideas, I spent 2 weeks tweaking the 3 different sized maps.. Now before a mission, you can plan out your approach much better.. I might even add SAM radius stuff, I don't know.. I wish TK had an option to turn on/off overlays in the Mission Menus..