I have exactly the same problem, and it's one of the many reasons I much prefer smaller empires with peaceful victory conditions.
The main problem is the civil unrest issue. Edit: Same with Pollution.
At the beginning of your turn the game gives you pop-ups of all your cities that are in civil unrest, but refuses to zoom-to-city like with other info-dumps at the beginning of the turn. So you have to memorize the list of names for when your turn starts proper and then scroll over your entire empire to find the visual clue of smoke over a city.
You could micromanage each city before your turn is over to ensure there is no unrest, but even this can get disrupted in a big empire war game as your troops die to something or other.
I'm not sure if this is something civassist helps with as I've never used that.
So I began experimenting with city names that helped to ease this problem of memory + location finding unrested cities in a large empire.
I'm sad to say, nothing seemed to work. I tried numbered systems, calling each town 1, 2, 3, 4 etc etc, I tried locational/numerical, calling each town Egypt 1, Egypt 2, Egypt 3 etc etc and a whole host of other ideas, but none of it really had any beneficial impact, I still found myself scrolling over my entire empire at the beginning and end of each turn, and, obviously, raging when I occasionally forgot to do this because I'm, alas, human.