At the start, when it's easy to remember stuff and I've only got a handful of provinces, I do everything manually, city by city.
When that gets complicated, I turn on auto-tax. I prefer that for larger empires since it will -usually- keep growth down a bit.
I will still scroll through every city every turn to make sure it's building something, when I have the cash. If I'm in a low cash flow situation, then I just target specific cities to keep them advancing, and build other non-essential stuff as needed.
One thing I've learned though. Even though cities are great cash, it's important to keep castles around. In my last English campaign, I kept only a single castle in each major border zone. When I lost that to the enemy, they were able to march all over my cities because I couldn't convert any of them back to castles and my other castle was too far away to do anything but provide moral support. I try to be a lot more careful now. :S
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