@Seamus I can only say how I am doing San Francisco.
I am focusing on the important parts.
What important parts? You may ask...
The ones important to the theme and story of the game.
For me that's The Presidio, it's Golden Gate Park, it's Alcatraz, It's Fisherman's Wharf and Pier 39, it's also Chinatown, the Aquarium, and a tiny bit of downtown.
Trying to map out an entire city is just silly, it's never going to all be used, so make what you're going to use.