Sometimes I fully control cities, sometimes I only partially do. It depends what's really necessary. I find that as far as GP are concerned, you really only need to worry about 1 or 2 cities and not make any in others. Typically the only ones I focus are either GE's or GS's.
In any case, there is a mod that can help with manual citizen control. By default, the game stops notifying you of population growth over 5 or so. You can make it notify you of new citizens forever with
Custom Notifications. Granted, you don't need it... you can watch every city every turn for growth if you want... but this is an option if you find that tedious. You can also set it to alert you of new cultural tile acquisitions. Very handy when you're in the mood to REALLY control every aspect of your cities. My only gripe with it is that upon loading save games, you get a bazillion notifications of every tile you've acquired in that game so far, but if you clear all messages before saving, then you can safely ignore the ones at loading and go to the next turn, at which point they'll disappear.